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From: Xiaqing Z. <zha...@gm...> - 2015-06-08 18:44:51
|
Hi, I am encountering similar issues as in this post when using SNVerPool.jar (version 0.5.3): http://seqanswers.com/forums/showthread.php?t=39991, where at some sites one of the samples shows NA:NA in the AD:DP entry. By samtools tviewing the particular bam file it seems that the coverage in the sample showing NA is not 0. Other tools such as Popoolation2 and VarScan are able to get non-zero reference and alternative allele read depths for the sample. I was using the same base quality and mapping quality thresholds when running SNVer and Popoolation/VarScan. So what could be the reason that SNVer gives NA entries in AD:DP? The only parameters I set manually were -mq 20 -bq 20 -t 0.01. Thanks, Xiaqing |
From: Fear, D. <dav...@kc...> - 2015-03-04 12:44:01
|
Hi, I'm trying to download SNVerGUI to a 64bit MAC running OS, the zipped file appears download ok (Mac OSX (cocoa/x86_64) - SNVerGUI.macosx.cocoa.x86_64.zip) but when I unpack the file it creates an empty folder. Could you please give me a pointer as to what I'm doing wrong. Many thanks Dr. David Fear Lecturer MRC & Asthma UK Centre in Allergic Mechanisms of Asthma Dept. of Respiratory Medicine and Allergy King's College London 5th. Floor, Tower Wing, Guy's Hospital St. Thomas Street London SE1 9RT Tel: 020 7188 0613 Fax: 020 7403 8640 |
From: Uebe, S. <Ste...@uk...> - 2014-07-07 18:14:45
|
Hi everyone, I'm probably not the first one to encounter this very cryptic error message. I have used SNVerIndividual without problems so far; but with one particular BED file, I get this message. I've quadruple-checked the BED file; there is absolutely nothing wrong with it. It's Chromosome, Tab, Start (0-based), Tab, End (0-based), Newline. I've tried different ways of sorting, all to no avail. At the moment, my only possible conclusions are that either there is an undocumented size limit on the BED file (at 4.7 Mb and 194,820 lines, this one is somewhat larger than the others), or this is a major bug that should be dealt with as soon as possible. Any suggestions are most welcome. Regards, Steffen Uebe Dr. rer. nat. Steffen Uebe Humangenetisches Institut Universitätsklinikum Erlangen Tel. +49-9131-85-26101<tel:+49-9131-85-26101> Fax +49-9131-85-23232<fax:+49-9131-85-23232> |
From: Sean M. <Sea...@uc...> - 2014-06-16 04:05:54
|
Hello, I have installed SNVerGUI on a windows 7 machine with Java 1.7.0. When I try to launch the GUI, I get an error stating it cannot find a runtime environment, in the path containing my install, but in a jre subdirectory (which doesn't exist in the install). Other Java programs work fine. Do I need to make that directory and install a 1.6 version there? If that's the case, I know your're not Java, but how? -Sean |
From: Antariksh T. <ant...@gm...> - 2014-05-31 11:10:46
|
HI Wei, I have checked the reference file and there is no problem with it ( downloaded from ensembl: ftp://ftp.ensemblgenomes.org/pub/release-22/plants/fasta/arabidopsis_thaliana/dna/) . It is the same file that was used for mapping the RNA seq data. Please help me resolve this issue of getting only "N" in Ref in the the output file. Thanks Antariksh |
From: Wei W. <ww...@us...> - 2014-05-29 21:17:06
|
Hi Antariksh, It is probably the reference issue, if there is "N" in the reference column. Did you check if you used the correct reference? Thanks, Wei On Thu, May 29, 2014 at 12:51 AM, Antariksh Tyagi <ant...@gm...> wrote: > Hi, > > Please help me resolve this problem! > > I ran my illumina RNAseq data of single pooled sequencing of 50 diploid *Arabidipsis > thaliana* (100 haploid genomes). But the output has only 'N' in Ref and > could not detect any SNP's. > The parameters I used are as follows: > > BQ: 20 > MQ: 30 > Haploids:100 > Others:default > > Am I using right parameters for SNP calling in this single pool data. If > yes then what could be the problem? > > Here attaching .vcf file from SNver and functional annotation file from > SNPeff. > > Thanks > > Antariksh Tyagi > CSIR-National Botanical Research Institute > India > > > ------------------------------------------------------------------------------ > Time is money. Stop wasting it! Get your web API in 5 minutes. > www.restlet.com/download > http://p.sf.net/sfu/restlet > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help > > |
From: Antariksh T. <ant...@gm...> - 2014-05-29 04:52:18
|
<!--========================================================================== FTL macros ========================================================================== --> <!--========================================================================== CSS styles ========================================================================== --> <style type="text/css"> body { background-color: #dddddd; } /* Table styles. */ table { border-color: #000; border-spacing: 0px; border-style: solid; border-width: 1px; cell-spacing: 0px; } .noBorder { border-width: 0px; } td, th { font-family: Arial, Helvetica, sans-serif; font-size: 10pt; padding: 2px 0.5em; white-space: nowrap; } td.numeric { text-align: right; } th { background-color: #c0c0c0; } th.mainHeader { background-color: #808080; color: #ffffff; text-align: left; } th a { color: #000080; text-decoration: none; } th a:visited { color: #000080; } th a:active, th a:hover { color: #800000; text-decoration: underline; } .toc { border: 1px solid #aaa; background-color: #eeeeee; padding: 5px; font-size: 95%; } .note { border: 1px solid #aaa; background-color: #eeeeee; padding: 5px; font-size: 90%; text-align: left; } .main { margin-top: 15px; width: 1000px; text-align: left; background: #ffffff; border: 3px solid #777777; } .histo { table-layout:fixed; width:100%; border:1px solid #aaa; word-wrap:break-word; } </style> <!--========================================================================== Index ========================================================================== --> <center> <div class="main"> <center> <h3> SnpEff: Variant analysis </h3> </center> <div style="margin-left: .5em"> <table class="toc"><tr><td> <center><b>Contents</b></center> <a href="#summary">Summary</a><br> <a href="#changeRateChr"> Change rate by chromosome</a><br> <a href="#changesByType">Variants by type</a><br> <a href="#effectsImpact"> Number of variants by impact </a><br> <a href="#effectsImpact"> Number of variants by functional class </a><br> <a href="#effects"> Number of variants by effect </a><br> <a href="#quality">Quality histogram</a><br> <a href="#coverage">Coverage histogram</a><br> <a href="#baseChages">Base change table</a><br> <a href="#tstv">Transition vs transversions (ts/tv)</a><br> <a href="#alleleFreq"> Frequency of alleles </a><br> <a href="#codonChanges"> Codon change table </a><br> <a href="#aaChanges"> Amino acid change table </a><br> <a href="#chrChanges"> Chromosome change plots </a><br> <a href="snpEff_genes.txt"> Details by gene </a><br> </tr></td></table> </div> <!--========================================================================== Summary table ========================================================================== --> <hr> <a name="summary"> <center> <b>Summary</b><p> <table border=0> <tr bgcolor=ffffff> <td valign=top> <b> Genome </b> </td> <td> athaliana130 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Date </b> </td> <td> 2014-05-29 10:24 </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> SnpEff version </b> </td> <td> <pre>SnpEff 3.5f (build 2014-03-18), by Pablo Cingolani</pre> </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Command line arguments </b> </td> <td> <pre>SnpEff athaliana130 input_Directory.all.filter_sample_1.vcf </pre> </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Warnings </b> </td> <td bgcolor="#ff0000"> 26 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Number of lines (input file) </b> </td> <td> 3,194 </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Number of variants (before filter) </b> </td> <td> 3,194 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Filter </b> </td> <td> </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Number of variants filtered out </b> </td> <td> 0 </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Number of not variants <br>(i.e. reference equals alternative) </b> </td> <td> 0 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Number of variants processed <br> (i.e. after filter and non-variants) </b> </td> <td> 3,194 </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Number of known variants <br>(i.e. non-empty ID) </b> </td> <td> 0 ( 0% ) </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Number of effects </b> </td> <td> 14,915 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Genome total length </b> </td> <td> 119,667,750 </td> </tr> <tr bgcolor=ffffff> <td valign=top> <b> Genome effective length </b> </td> <td> 119,667,750 </td> </tr> <tr bgcolor=dddddd> <td valign=top> <b> Change rate </b> </td> <td> 1 change every 37,466 bases </td> </tr> </table> <p> </center> <!--========================================================================== Change rate by chromosome ========================================================================== --> <hr> <a name="changeRateChr"> <center> <b> Change rate details </b><p> <table border=1> <tr><th> Chromosome </th><th> Length </th><th> Changes </th><th> Change rate </th></tr> <tr> <td> 1 </td> <td class="numeric"> 30,427,671 </td> <td class="numeric"> 815 </td> <td class="numeric"> 37,334 </td> </tr> <tr> <td> 2 </td> <td class="numeric"> 19,698,289 </td> <td class="numeric"> 449 </td> <td class="numeric"> 43,871 </td> </tr> <tr> <td> 3 </td> <td class="numeric"> 23,459,830 </td> <td class="numeric"> 599 </td> <td class="numeric"> 39,164 </td> </tr> <tr> <td> 4 </td> <td class="numeric"> 18,585,056 </td> <td class="numeric"> 530 </td> <td class="numeric"> 35,066 </td> </tr> <tr> <td> 5 </td> <td class="numeric"> 26,975,502 </td> <td class="numeric"> 792 </td> <td class="numeric"> 34,059 </td> </tr> <tr> <td> Mt </td> <td class="numeric"> 366,924 </td> <td class="numeric"> 7 </td> <td class="numeric"> 52,417 </td> </tr> <tr> <td> Pt </td> <td class="numeric"> 154,478 </td> <td class="numeric"> 2 </td> <td class="numeric"> 77,239 </td> </tr> <tr> <th> Total </th> <th class="numeric"> 119,667,750 </th> <th class="numeric"> 3,194 </th> <th class="numeric"> 37,466 </th> </tr> </table> </center> <!--========================================================================== Changes by type ========================================================================== --> <hr> <a name="changesByType"> <center> <b> Number changes by type</b><p> <table border=1> <thead> <tr> <th> <b> Type </b> </th> <th> <b> Total </b> </th> <th> <b> Homo </b> </th> <th> <b> Hetero </b> </th> </tr> </thead> <tbody> <tr> <td> <b> SNP </b> </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <td> <b> MNP </b> </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <td> <b> INS </b> </td> <td class="numeric" bgcolor="#00ff00"> 1,289 </td> <td class="numeric" bgcolor="#00ff00"> 1,289 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <td> <b> DEL </b> </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <td> <b> MIXED </b> </td> <td class="numeric" bgcolor="#ff0000"> 1,905 </td> <td class="numeric" bgcolor="#ff0000"> 1,905 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <td> <b> Interval </b> </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> <td class="numeric" bgcolor="ffffff"> 0 </td> </tr> </tbody> <tfoot> <tr> <th><b>Total </b> </th> <th class="numeric"> 3,194 </th> <th class="numeric"> 3,194 </th> <th class="numeric"> 0 </th> </tr> </tfoot> </table> </center> <!--========================================================================== Effects by impact ========================================================================== --> <hr> <a name="effectsImpact"> <center> <b> Number of effects by impact </b> <p> <table border=0> <thead> <tr> <th><b> Type (alphabetical order) </b></th> <th> </th> <th> Count </th> <th> Percent </th> </tr> </thead> <tr> <td> <b> HIGH </b> </td> <th> </th> <td class="numeric" bgcolor="#01fd00"> 163 </td> <td class="numeric" bgcolor="#01fd00"> 1.093% </td> </tr> <tr> <td> <b> LOW </b> </td> <th> </th> <td class="numeric" bgcolor="#00ff00"> 50 </td> <td class="numeric" bgcolor="#00ff00"> 0.335% </td> </tr> <tr> <td> <b> MODIFIER </b> </td> <th> </th> <td class="numeric" bgcolor="#ff0000"> 14,702 </td> <td class="numeric" bgcolor="#ff0000"> 98.572% </td> </tr> </table><br> <p> </center> <!--========================================================================== Effects by functional class ========================================================================== --> <hr> <a name="effectsFuncClass"> <center> <b> Number of effects by functional class </b> <p> <table border=0> <thead> <tr> <th><b> Type (alphabetical order) </b></th> <th> </th> <th> Count </th> <th> Percent </th> </tr> </thead> </table><br> <p> Missense / Silent ratio: </th><td class="numeric"> ? </center> <!--========================================================================== Effects stats ========================================================================== --> <hr> <a name="effects"> <center> <b> Number of effects by type and region </b> <p> <table border=0> <tr> <th> Type </th> <th> Region </th> </tr> <tr> <td> <table border=0> <thead> <tr> <th><b> Type (alphabetical order) </b></th> <th> </th> <th> Count </th> <th> Percent </th> </tr> </thead> <tr> <td> <b> DOWNSTREAM </b> </td> <th> </th> <td class="numeric" bgcolor="#ff0000"> 5,579 </td> <td class="numeric" bgcolor="#ff0000"> 37.405% </td> </tr> <tr> <td> <b> EXON </b> </td> <th> </th> <td class="numeric" bgcolor="#02fc00"> 61 </td> <td class="numeric" bgcolor="#02fc00"> 0.409% </td> </tr> <tr> <td> <b> FRAME_SHIFT </b> </td> <th> </th> <td class="numeric" bgcolor="#05f900"> 120 </td> <td class="numeric" bgcolor="#05f900"> 0.805% </td> </tr> <tr> <td> <b> INTERGENIC </b> </td> <th> </th> <td class="numeric" bgcolor="#07f700"> 178 </td> <td class="numeric" bgcolor="#07f700"> 1.193% </td> </tr> <tr> <td> <b> INTRAGENIC </b> </td> <th> </th> <td class="numeric" bgcolor="#02fc00"> 53 </td> <td class="numeric" bgcolor="#02fc00"> 0.355% </td> </tr> <tr> <td> <b> INTRON </b> </td> <th> </th> <td class="numeric" bgcolor="#0bf300"> 256 </td> <td class="numeric" bgcolor="#0bf300"> 1.716% </td> </tr> <tr> <td> <b> SPLICE_SITE_ACCEPTOR </b> </td> <th> </th> <td class="numeric" bgcolor="#00fe00"> 10 </td> <td class="numeric" bgcolor="#00fe00"> 0.067% </td> </tr> <tr> <td> <b> SPLICE_SITE_DONOR </b> </td> <th> </th> <td class="numeric" bgcolor="#00fe00"> 12 </td> <td class="numeric" bgcolor="#00fe00"> 0.08% </td> </tr> <tr> <td> <b> SPLICE_SITE_REGION </b> </td> <th> </th> <td class="numeric" bgcolor="#01fd00"> 50 </td> <td class="numeric" bgcolor="#01fd00"> 0.335% </td> </tr> <tr> <td> <b> START_LOST </b> </td> <th> </th> <td class="numeric" bgcolor="#00fe00"> 13 </td> <td class="numeric" bgcolor="#00fe00"> 0.087% </td> </tr> <tr> <td> <b> STOP_LOST </b> </td> <th> </th> <td class="numeric" bgcolor="#00ff00"> 8 </td> <td class="numeric" bgcolor="#00ff00"> 0.054% </td> </tr> <tr> <td> <b> UPSTREAM </b> </td> <th> </th> <td class="numeric" bgcolor="#e31b00"> 4,979 </td> <td class="numeric" bgcolor="#e31b00"> 33.383% </td> </tr> <tr> <td> <b> UTR_3_PRIME </b> </td> <th> </th> <td class="numeric" bgcolor="#6f8f00"> 2,440 </td> <td class="numeric" bgcolor="#6f8f00"> 16.359% </td> </tr> <tr> <td> <b> UTR_5_PRIME </b> </td> <th> </th> <td class="numeric" bgcolor="#34ca00"> 1,156 </td> <td class="numeric" bgcolor="#34ca00"> 7.751% </td> </tr> </table><br> </td> <td> <table border=0> <thead> <tr> <th><b> Type (alphabetical order) </b></th> <th> </th> <th> Count </th> <th> Percent </th> </tr> </thead> <tr> <td> <b> DOWNSTREAM </b> </td> <th> </th> <td class="numeric" bgcolor="#ff0000"> 5,579 </td> <td class="numeric" bgcolor="#ff0000"> 37.405% </td> </tr> <tr> <td> <b> EXON </b> </td> <th> </th> <td class="numeric" bgcolor="#08f600"> 202 </td> <td class="numeric" bgcolor="#08f600"> 1.354% </td> </tr> <tr> <td> <b> INTERGENIC </b> </td> <th> </th> <td class="numeric" bgcolor="#07f700"> 178 </td> <td class="numeric" bgcolor="#07f700"> 1.193% </td> </tr> <tr> <td> <b> INTRON </b> </td> <th> </th> <td class="numeric" bgcolor="#0bf300"> 256 </td> <td class="numeric" bgcolor="#0bf300"> 1.716% </td> </tr> <tr> <td> <b> NONE </b> </td> <th> </th> <td class="numeric" bgcolor="#01fd00"> 53 </td> <td class="numeric" bgcolor="#01fd00"> 0.355% </td> </tr> <tr> <td> <b> SPLICE_SITE_ACCEPTOR </b> </td> <th> </th> <td class="numeric" bgcolor="#00ff00"> 10 </td> <td class="numeric" bgcolor="#00ff00"> 0.067% </td> </tr> <tr> <td> <b> SPLICE_SITE_DONOR </b> </td> <th> </th> <td class="numeric" bgcolor="#00fe00"> 12 </td> <td class="numeric" bgcolor="#00fe00"> 0.08% </td> </tr> <tr> <td> <b> SPLICE_SITE_REGION </b> </td> <th> </th> <td class="numeric" bgcolor="#01fd00"> 50 </td> <td class="numeric" bgcolor="#01fd00"> 0.335% </td> </tr> <tr> <td> <b> UPSTREAM </b> </td> <th> </th> <td class="numeric" bgcolor="#e31b00"> 4,979 </td> <td class="numeric" bgcolor="#e31b00"> 33.383% </td> </tr> <tr> <td> <b> UTR_3_PRIME </b> </td> <th> </th> <td class="numeric" bgcolor="#6f8f00"> 2,440 </td> <td class="numeric" bgcolor="#6f8f00"> 16.359% </td> </tr> <tr> <td> <b> UTR_5_PRIME </b> </td> <th> </th> <td class="numeric" bgcolor="#34ca00"> 1,156 </td> <td class="numeric" bgcolor="#34ca00"> 7.751% </td> </tr> </table><br> </td> </tr> </table> <p> <img src="http://chart.apis.google.com/chart?cht=bvs&chbh=50,4,8&chs=800x300&chxt=y,y,x,x&chtt=Variations&chxp=1,50.0|3,50.0&chxr=0,0.0,37.40529668119343|1,0.0,100.0|3,0.0,100.0&chco=00FFFF,FA8072,FF0000,A52A2A,FFA500,DEB887,E9967A,7FFFD4,808080&chdl=Upstream|5%27UTR|Exon|Splice+Donor|Intron|Splice+Acceptor|3%27UTR|Downstream|Intergenic&chxl=1:|%25|2:|Intergenic|Up|5%27UTR|Exon|Donor|Intron|Acceptor|Exon|3%27UTR|Down|Intergenic|3:|&chd=e:AA5HAAAAAAAAAAAAAAAAAA,AAAANRAAAAAAAAAAAAAAAA,AAAAAACUAAAAAACUAAAAAA,AAAAAAAAAJAAAAAAAAAAAA,AAAAAAAAAAC8AAAAAAAAAA,AAAAAAAAAAAAAHAAAAAAAA,AAAAAAAAAAAAAAAAb.AAAA,AAAAAAAAAAAAAAAAAA..AA,CDAAAAAAAAAAAAAAAAAACD" border=1><p> </center> <!--========================================================================== Quality plots ========================================================================== --> <hr> <a name="quality"> <b> Quality: </b> <p> <pre> <table class="histo"> <tr> <th width=15%>Min</th><td>0</td> </tr> <tr> <th>Max</th><td>0</td> </tr> <tr> <th>Mean</th><td>0</td> </tr> <tr> <th>Median</th><td>0</td> </tr> <tr> <th>Standard deviation</th><td>0</td> </tr> <tr> <th>Values</th><td>0</td> </tr> <tr> <th>Count</th><td>3194</td> </tr> </tr> </table> <img src="http://chart.apis.google.com/chart?cht=bvg&chd=e:..&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chtt=Quality+histogram&chxl=1:|Count|2:|0|3:|Quality&chxr=0,0.0,3194.0|1,0.0,100.0|3,0.0,100.0"><br> </pre> <!--========================================================================== Coverage ========================================================================== --> <hr> <a name="coverage"> <b> Coverage:</b> <p> <pre> <table class="histo"> <tr> <th width=15%>Min</th><td>5</td> </tr> <tr> <th>Max</th><td>33,222</td> </tr> <tr> <th>Mean</th><td>128.886</td> </tr> <tr> <th>Median</th><td>37</td> </tr> <tr> <th>Standard deviation</th><td>691.317</td> </tr> <tr> <th>Values</th><td>5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,177,178,179,181,184,186,187,188,189,190,191,192,193,194,195,196,198,199,201,202,203,204,206,207,209,210,211,212,213,214,215,216,218,220,221,222,223,225,226,227,228,229,231,232,234,235,236,237,240,241,243,244,245,246,247,249,250,251,252,254,255,256,257,258,259,261,263,264,268,269,270,271,272,273,275,276,277,278,279,280,281,282,283,285,286,287,289,290,291,293,295,296,297,300,301,304,305,307,308,309,310,311,313,314,319,324,326,329,330,335,336,338,339,340,341,342,343,346,348,350,351,352,355,356,357,364,365,366,367,368,369,372,377,380,384,386,387,391,393,395,397,398,400,401,404,405,406,407,409,411,412,414,416,417,418,420,421,429,437,440,441,443,448,449,450,452,456,457,459,460,461,464,472,473,474,476,477,480,482,487,491,494,496,505,506,511,514,518,519,524,530,531,544,551,560,562,566,567,576,578,590,594,595,603,606,607,610,620,627,629,637,650,654,655,658,663,665,672,678,690,691,696,698,708,709,710,713,720,722,724,727,729,736,745,773,774,782,787,791,797,808,815,816,839,841,861,888,896,901,903,908,915,920,928,934,986,1004,1008,1039,1057,1070,1080,1095,1099,1124,1142,1149,1189,1210,1245,1249,1255,1260,1262,1290,1294,1380,1386,1401,1402,1430,1440,1466,1492,1513,1591,1670,1704,1742,1770,1933,2021,2243,2596,2829,2961,3074,3118,3234,3517,3731,4193,5216,6437,12492,33222</td> </tr> <tr> <th>Count</th><td>72,119,60,79,89,83,74,69,60,54,51,47,44,45,56,43,44,44,48,42,38,32,29,26,28,35,33,34,16,29,27,33,29,15,25,25,24,16,22,22,17,17,22,14,18,10,24,15,19,12,14,16,15,10,10,12,13,12,15,12,13,13,13,10,15,16,11,11,12,7,13,9,10,11,12,12,5,15,4,7,6,6,7,7,7,14,7,10,6,6,14,5,11,10,4,5,6,5,7,5,5,5,8,10,6,3,10,8,4,2,3,10,7,4,8,2,6,5,4,5,1,6,5,3,6,6,5,7,6,2,2,4,1,4,3,2,10,5,8,3,4,1,1,2,5,6,3,2,5,3,2,5,3,5,4,4,5,3,3,1,2,5,6,2,3,3,5,1,5,5,2,2,1,7,5,2,6,7,2,1,4,1,2,4,5,3,1,6,1,4,1,2,2,2,1,1,1,2,2,5,3,1,1,3,2,3,1,1,3,3,1,1,2,4,1,4,3,3,1,3,1,1,2,2,1,1,1,2,1,1,3,2,3,1,2,4,1,3,1,1,1,3,2,1,1,2,2,2,2,1,2,1,1,2,1,2,1,2,1,2,1,1,3,1,2,4,1,1,2,1,1,1,3,1,3,2,1,1,1,2,2,1,1,1,1,2,1,1,1,2,2,1,1,1,1,1,1,2,1,1,1,1,1,2,2,1,2,1,2,2,1,2,2,1,1,3,1,1,2,1,3,1,1,1,1,1,1,2,1,1,2,1,2,2,2,2,1,1,1,3,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,2,1,1,1,2,2,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,2,2,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1</td> </tr> </tr> </table> <img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chg=3321.0,19.0,3,2&chtt=Coverage+histogram&chxr=0,1.0,191.0|1,0.0,100.0|3,0.0,100.0&chxl=1:|Count|2:|5||||||||||||||||||||||||||||||53||||||||||||||||||||||||||||||101||||||||||||||||||||||||||||||148||||||||||||||||||||||||||||||204||||||||||||||||||||||||||||||268||||||||||||||||||||||||||||||344||||||||||||||||||||||||||||||450||||||||||||||||||||||||||||||652||||||||||||||||||||||||||||||1057|||||||||||||||||||||||||||||33222|3:|Coverage&chd=e:..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"><br> </pre> <!--========================================================================== InDels ========================================================================== --> <hr> <b> Insertions and deletions length:</b> <p> <pre> <table class="histo"> <tr> <th width=15%>Min</th><td>1</td> </tr> <tr> <th>Max</th><td>2</td> </tr> <tr> <th>Mean</th><td>1.164</td> </tr> <tr> <th>Median</th><td>1</td> </tr> <tr> <th>Standard deviation</th><td>0.37</td> </tr> <tr> <th>Values</th><td>1,2</td> </tr> <tr> <th>Count</th><td>1078,211</td> </tr> </tr> </table> <img src="http://chart.apis.google.com/chart?cht=bvg&chbh=8,4,2&chd=e:..AA&chs=800x300&chxt=y,y,x,x&chxp=1,50.0|3,50.0&chxl=1:|Count|2:|1|2|3:|Length&chtt=Insertion+deletion+length+histogram&chxr=0,211.0,1078.0|1,0.0,100.0|3,0.0,100.0"><br> </pre> <!--========================================================================== Base changes ========================================================================== --> <hr> <a name="baseChages"> <center> <b> Base changes (SNPs) </b> <p> <table border=1> <tr> <td> </td> <th> <b> A </b> </th> <th> <b> C </b> </th> <th> <b> G </b> </th> <th> <b> T </b> </th> </tr> <tr> <th> <b> A </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <th> <b> C </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <th> <b> G </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr> <tr> <th> <b> T </b> </th><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td><td class="numeric" bgcolor="ffffff"> 0 </td> </tr> </table> </center> <p> <!--========================================================================== Ts/Tv ========================================================================== --> <hr> <a name="tstv"> <center> <b> Ts/Tv (transitions / transversions) </b> <p> </center> <small> <b>Note:</b> Only SNPs are used for this statistic.<br> <b>Note:</b> This Ts/Tv ratio is a 'raw' ratio. Some people prefer to use a ratio of rates, not observed events. In that case, you need to multiply by 2.0 (since there are twice as many possible transitions than transversions, E[Ts/Tv] ratio is twice the ratio of events). </small> <p> <center> <table border=1> <tr> <th> Transitions </th><td class="numeric"> 0 </td> </tr> <tr> <th> Transversions </th><td class="numeric"> 0 </td> </tr> <tr> <th> Ts/Tv ratio </th><td class="numeric"> 0 </td> </tr> </table> </center> <p> <p> <!--========================================================================== Allele frequency ========================================================================== --> <hr> <a name="alleleFreq"> <center> <b> Frequency of alleles </b> <p> </center> Note: Number of times an allele appears once (singleton), twice (doubletons), etc.<p> <p> <!--========================================================================== Codon change table ========================================================================== --> <hr> <a name="codonChanges"> <center> <b> Codon changes</b> <p> <div class="note"> How to read this table: <br> - Rows are reference codons and columns are changed codons. E.g. Row 'AAA' column 'TAA' indicates how many 'AAA' codons have been replaced by 'TAA' codons.<br> - Red background colors indicate that more changes happened (heat-map).<br> - Diagonals are indicated using grey background color <br> - WARNING: This table may include different translation codon tables (e.g. mamalian DNA and mitochondrial DNA).<br> <p> </div><p> <table border=1> <thead> <tr> <th> </th> <th> -AA </th> <th> -AC </th> <th> -CC </th> <th> -GG </th> <th> -NA </th> <th> -NC </th> <th> -NG </th> <th> -NT </th> <th> -TG </th> <th> -TT </th> <th> A-C </th> <th> A-G </th> <th> A-T </th> <th> AA- </th> <th> AAA </th> <th> AAC </th> <th> AAG </th> <th> AAT </th> <th> AC- </th> <th> ACA </th> <th> ACC </th> <th> ACG </th> <th> ACN </th> <th> AG- </th> <th> AGG </th> <th> AGT </th> <th> AN- </th> <th> AT- </th> <th> ATA </th> <th> ATC </th> <th> ATG </th> <th> ATT </th> <th> C-A </th> <th> C-N </th> <th> CA- </th> <th> CAA </th> <th> CAG </th> <th> CAT </th> <th> CC- </th> <th> CCA </th> <th> CCT </th> <th> CGG </th> <th> CGT </th> <th> CT- </th> <th> CTA </th> <th> CTC </th> <th> CTT </th> <th> G-A </th> <th> G-C </th> <th> G-N </th> <th> G-T </th> <th> GAA </th> <th> GAC </th> <th> GAG </th> <th> GAN </th> <th> GCC </th> <th> GG- </th> <th> GGA </th> <th> GGG </th> <th> GTT </th> <th> T-A </th> <th> T-C </th> <th> T-G </th> <th> TAA </th> <th> TAC </th> <th> TAT </th> <th> TC- </th> <th> TCA </th> <th> TCC </th> <th> TCG </th> <th> TCN </th> <th> TCT </th> <th> TG- </th> <th> TGA </th> <th> TGG </th> <th> TGT </th> <th> TN- </th> <th> TT- </th> <th> TTA </th> <th> TTC </th> <th> TTG </th> <th> TTT </th> </tr> </thead> <tr> <th> -AA </th> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -AC </th> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -CC </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -GG </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -NA </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -NC </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> </tr> <tr> <th> -NG </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <th class="numeric">   </th> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric" bgcolor="ffffff">   </td> <td class="numeric... [truncated message content] |
From: Wei W. <ww...@us...> - 2014-04-03 17:56:45
|
Hi King, Thanks for reporting this issue. In fact, the problem is when you download the bam file directly from web browser, the file will be truncated. The SNVer website has been updated to avoid this issue. Please have a try again. Cheers, Wei On Tue, Apr 1, 2014 at 11:02 PM, King Robert <rob...@gm...>wrote: > Hi, Wei, > I am trying snver under windows 7, jre1.6: > > I am using: java -Xmx2g -jar SNVerIndividual.jar -i .\test1\test1.bam -r > g:\chrx.fa > and it tells me: > > Input bam file is : .\test1\test1.bam > Output result file is : .\test1\test1.bam.raw.vcf, > .\test1\test1.bam.indel.raw.vcf > > net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not > enough fields; File .\test1\test1.bam; Line 1 > Line: BAM : > > if I use sam file, it is fine, so it should be something with bam file > handling? > > This happens to both snver and snverGUI, > > Could you please find a solution? Thank you! > > Bob > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help > > |
From: King R. <rob...@gm...> - 2014-04-02 05:19:54
|
Hi, Wei, I didn't find how to reply in this mailing list, so I have to open a new thread. I found the cause to the bam parsing error. It is the format error of the bam files in the sample data! So I suggest to include a valid bam files in your web to avoid future confusion. thanks. Bob |
From: King R. <rob...@gm...> - 2014-04-02 03:02:21
|
Hi, Wei, I am trying snver under windows 7, jre1.6: I am using: java -Xmx2g -jar SNVerIndividual.jar -i .\test1\test1.bam -r g:\chrx.fa and it tells me: Input bam file is : .\test1\test1.bam Output result file is : .\test1\test1.bam.raw.vcf, .\test1\test1.bam.indel.raw.vcf net.sf.samtools.SAMFormatException: Error parsing text SAM file. Not enough fields; File .\test1\test1.bam; Line 1 Line: BAM: if I use sam file, it is fine, so it should be something with bam file handling? This happens to both snver and snverGUI, Could you please find a solution? Thank you! Bob |
From: Namrata P. <nam...@gm...> - 2014-01-24 11:07:46
|
Hii, How can i call consensus using SNVer? Thank you in advance for any help... |
From: Marty K. <mar...@gm...> - 2013-12-27 06:59:55
|
Helly Wei; I am using SNVer to call variants on pooled sequence data. I get the following error: Collecting total number of reads... Cannot read split target file by tabjava.io.IOException: Cannot read split target file by tab at net.sf.snver.pileup.loader.FilterReader.<init>(FilterReader.java:56) at net.sf.snver.pileup.loader.Peeker.<init>(Peeker.java:123) at net.sf.snver.pileup.SNVerPool._pileup(SNVerPool.java:149) at net.sf.snver.pileup.SNVerPool.pileup(SNVerPool.java:62) at net.sf.snver.pileup.SNVerPool.main(SNVerPool.java:56) Can you tell me what could be causing this? Thanks! -- Marty Kardos PhD candidate Montana Conservation Genetics Lab NSF Montana Ecology of Infectious Disease IGERT trainee Graduate Fellow of the Montana Institute on Ecosystems University of Montana |
From: WangWei <bo...@ho...> - 2013-12-11 02:44:35
|
Hi Sara, Have you tried Java 1.6.0? SNVerGUI was build on Java 1.6, may have compatibility problems with Java 1.7. Thanks, Wei Date: Tue, 10 Dec 2013 20:03:12 +0100 From: sor...@un... To: snv...@li... Subject: [Snver-help] SNVer-GUI Hi, I am trying SNVer-Gui for pooled sequencing with the example data in Windows 7 with java 1.7.0_25 version. When the process finishes I get this message: Could not create the view: For input string: "0,420" ava.lang.NumberFormatException: For input string: "0,420" at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source) at java.lang.Float.valueOf(Unknown Source) at net.sf.snver.gui.riena.model.VcfBean.makeInfoProperties(VcfBean.java:109) at net.sf.snver.gui.riena.model.VcfBean.setInfo(VcfBean.java:97) at net.sf.snver.gui.riena.model.VcfBeanFactory.makeBean(VcfBeanFactory.java:26) at net.sf.snver.gui.riena.util.VcfReader.readList(VcfReader.java:60) at net.sf.snver.gui.riena.util.VcfReader.<init>(VcfReader.java:41) at net.sf.snver.gui.riena.controller.VcfController.<init>(VcfController.java:38) at net.sf.snver.gui.riena.view.ResultView.createController(ResultView.java:65) at net.sf.snver.gui.riena.view.ResultView.createController(ResultView.java:1) at org.eclipse.riena.navigation.ui.swt.views.SubModuleView.createPartControl(SubModuleView.java:218) at org.eclipse.ui.internal.ViewReference.createPartHelper(ViewReference.java:375) at org.eclipse.ui.internal.ViewReference.createPart(ViewReference.java:229) at org.eclipse.ui.internal.WorkbenchPartReference.getPart(WorkbenchPartReference.java:595) at org.eclipse.ui.internal.Perspective.showView(Perspective.java:2245) at org.eclipse.ui.internal.WorkbenchPage.busyShowView(WorkbenchPage.java:1145) at org.eclipse.ui.internal.WorkbenchPage$20.run(WorkbenchPage.java:3921) at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70) at org.eclipse.ui.internal.WorkbenchPage.showView(WorkbenchPage.java:3918) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.prepareView(SubApplicationView.java:716) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.prepareView(SubApplicationView.java:693) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.access$2(SubApplicationView.java:692) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView$MySubModuleNodeListener.activated(SubApplicationView.java:570) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView$MySubModuleNodeListener.activated(SubApplicationView.java:1) at org.eclipse.riena.navigation.listener.NavigationTreeObserver$MySubModuleNodeListener.activated(NavigationTreeObserver.java:1008) at org.eclipse.riena.navigation.listener.NavigationTreeObserver$MySubModuleNodeListener.activated(NavigationTreeObserver.java:1) at org.eclipse.riena.navigation.model.NavigationNode.notifyActivated(NavigationNode.java:198) at org.eclipse.riena.navigation.model.NavigationNode.activate(NavigationNode.java:799) at org.eclipse.riena.navigation.model.NavigationProcessor.activate(NavigationProcessor.java:1136) at org.eclipse.riena.navigation.model.NavigationProcessor.activate(NavigationProcessor.java:118) at org.eclipse.riena.navigation.model.NavigationNode.activate(NavigationNode.java:435) at org.eclipse.riena.navigation.model.NavigationProcessor.navigateSync(NavigationProcessor.java:445) at org.eclipse.riena.navigation.model.NavigationProcessor.jump(NavigationProcessor.java:592) at org.eclipse.riena.navigation.model.NavigationNode.jump(NavigationNode.java:1108) at org.eclipse.riena.navigation.model.NavigationNode.jump(NavigationNode.java:1104) at net.sf.snver.gui.riena.controller.ConsoleController$4.run(ConsoleController.java:243) at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35) at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135) at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4140) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3757) at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696) at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660) at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494) at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332) at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667) at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149) at org.eclipse.riena.navigation.ui.swt.application.SwtApplication.createView(SwtApplication.java:72) at org.eclipse.riena.navigation.ui.application.AbstractApplication.start(AbstractApplication.java:79) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577) at org.eclipse.equinox.launcher.Main.run(Main.java:1410) Can anybody tell me how can I solve this problem? Should I install java 1.6.0_30 instead of the version I have already? Thank you so much for your help, Best, Sara. ------------------------------------------------------------------------------ Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, & PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349831&iu=/4140/ostg.clktrk _______________________________________________ Snver-help mailing list Snv...@li... https://lists.sourceforge.net/lists/listinfo/snver-help |
From: Sara O. <sor...@un...> - 2013-12-10 19:23:38
|
Hi, I am trying SNVer-Gui for pooled sequencing with the example data in Windows 7 with java 1.7.0_25 version. When the process finishes I get this message: Could not create the view: For input string: "0,420" ava.lang.NumberFormatException: For input string: "0,420" at sun.misc.FloatingDecimal.readJavaFormatString(Unknown Source) at java.lang.Float.valueOf(Unknown Source) at net.sf.snver.gui.riena.model.VcfBean.makeInfoProperties(VcfBean.java:109) at net.sf.snver.gui.riena.model.VcfBean.setInfo(VcfBean.java:97) at net.sf.snver.gui.riena.model.VcfBeanFactory.makeBean(VcfBeanFactory.java:26) at net.sf.snver.gui.riena.util.VcfReader.readList(VcfReader.java:60) at net.sf.snver.gui.riena.util.VcfReader.<init>(VcfReader.java:41) at net.sf.snver.gui.riena.controller.VcfController.<init>(VcfController.java:38) at net.sf.snver.gui.riena.view.ResultView.createController(ResultView.java:65) at net.sf.snver.gui.riena.view.ResultView.createController(ResultView.java:1) at org.eclipse.riena.navigation.ui.swt.views.SubModuleView.createPartControl(SubModuleView.java:218) at org.eclipse.ui.internal.ViewReference.createPartHelper(ViewReference.java:375) at org.eclipse.ui.internal.ViewReference.createPart(ViewReference.java:229) at org.eclipse.ui.internal.WorkbenchPartReference.getPart(WorkbenchPartReference.java:595) at org.eclipse.ui.internal.Perspective.showView(Perspective.java:2245) at org.eclipse.ui.internal.WorkbenchPage.busyShowView(WorkbenchPage.java:1145) at org.eclipse.ui.internal.WorkbenchPage$20.run(WorkbenchPage.java:3921) at org.eclipse.swt.custom.BusyIndicator.showWhile(BusyIndicator.java:70) at org.eclipse.ui.internal.WorkbenchPage.showView(WorkbenchPage.java:3918) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.prepareView(SubApplicationView.java:716) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.prepareView(SubApplicationView.java:693) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView.access$2(SubApplicationView.java:692) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView$MySubModuleNodeListener.activated(SubApplicationView.java:570) at org.eclipse.riena.navigation.ui.swt.views.SubApplicationView$MySubModuleNodeListener.activated(SubApplicationView.java:1) at org.eclipse.riena.navigation.listener.NavigationTreeObserver$MySubModuleNodeListener.activated(NavigationTreeObserver.java:1008) at org.eclipse.riena.navigation.listener.NavigationTreeObserver$MySubModuleNodeListener.activated(NavigationTreeObserver.java:1) at org.eclipse.riena.navigation.model.NavigationNode.notifyActivated(NavigationNode.java:198) at org.eclipse.riena.navigation.model.NavigationNode.activate(NavigationNode.java:799) at org.eclipse.riena.navigation.model.NavigationProcessor.activate(NavigationProcessor.java:1136) at org.eclipse.riena.navigation.model.NavigationProcessor.activate(NavigationProcessor.java:118) at org.eclipse.riena.navigation.model.NavigationNode.activate(NavigationNode.java:435) at org.eclipse.riena.navigation.model.NavigationProcessor.navigateSync(NavigationProcessor.java:445) at org.eclipse.riena.navigation.model.NavigationProcessor.jump(NavigationProcessor.java:592) at org.eclipse.riena.navigation.model.NavigationNode.jump(NavigationNode.java:1108) at org.eclipse.riena.navigation.model.NavigationNode.jump(NavigationNode.java:1104) at net.sf.snver.gui.riena.controller.ConsoleController$4.run(ConsoleController.java:243) at org.eclipse.swt.widgets.RunnableLock.run(RunnableLock.java:35) at org.eclipse.swt.widgets.Synchronizer.runAsyncMessages(Synchronizer.java:135) at org.eclipse.swt.widgets.Display.runAsyncMessages(Display.java:4140) at org.eclipse.swt.widgets.Display.readAndDispatch(Display.java:3757) at org.eclipse.ui.internal.Workbench.runEventLoop(Workbench.java:2696) at org.eclipse.ui.internal.Workbench.runUI(Workbench.java:2660) at org.eclipse.ui.internal.Workbench.access$4(Workbench.java:2494) at org.eclipse.ui.internal.Workbench$7.run(Workbench.java:674) at org.eclipse.core.databinding.observable.Realm.runWithDefault(Realm.java:332) at org.eclipse.ui.internal.Workbench.createAndRunWorkbench(Workbench.java:667) at org.eclipse.ui.PlatformUI.createAndRunWorkbench(PlatformUI.java:149) at org.eclipse.riena.navigation.ui.swt.application.SwtApplication.createView(SwtApplication.java:72) at org.eclipse.riena.navigation.ui.application.AbstractApplication.start(AbstractApplication.java:79) at org.eclipse.equinox.internal.app.EclipseAppHandle.run(EclipseAppHandle.java:196) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.runApplication(EclipseAppLauncher.java:110) at org.eclipse.core.runtime.internal.adaptor.EclipseAppLauncher.start(EclipseAppLauncher.java:79) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:344) at org.eclipse.core.runtime.adaptor.EclipseStarter.run(EclipseStarter.java:179) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(Unknown Source) at sun.reflect.DelegatingMethodAccessorImpl.invoke(Unknown Source) at java.lang.reflect.Method.invoke(Unknown Source) at org.eclipse.equinox.launcher.Main.invokeFramework(Main.java:622) at org.eclipse.equinox.launcher.Main.basicRun(Main.java:577) at org.eclipse.equinox.launcher.Main.run(Main.java:1410) Can anybody tell me how can I solve this problem? Should I install java 1.6.0_30 instead of the version I have already? Thank you so much for your help, Best, Sara. |
From: Hyun Ji N. <no...@br...> - 2013-06-28 21:58:53
|
Hi, I'm testing SNVer to call variants from pooled sequence data, but I get an error message at the "Ready for pileup..." stage. I use the command: java -jar /path/SNVerPool.jar -i /path2bam/ -n 32 -r hg19.fasta -l target_hg19.bed -o test -t 0 Then I get: Input bam directory is : /path2bam/ Output result file is : test.raw.vcf, test.indel.raw.vcf Collecting total number of reads... =========>10%=========>20%=========>30%=========>40%=========>50%=========>60%=========>70%=========>80%=========>90%=========/seq/path/test.bam:HAPLOIDS[32]MQ[20]BQ[17] Ready for pileup... Progress: 0%>100%The Total File Size is Empty!! Time usage is 864 seconds Done! Then I only get vcf files with only headers but without any variant calls. Could you advise me on how to resolve this issue? Many thanks, Hyunji -- Dr Hyun Ji Noh Postdoctoral Associate Broad Institute of MIT and Harvard 5 Cambridge Center (Room 1316A) Cambridge, MA 02142 USA Phone: +1(617)714-7863 Email: no...@br... |
From: Hyun Ji N. <no...@br...> - 2013-06-28 19:39:35
|
Hi, I'm trying to use SNVer to call variants in my pooled sequencing data. My bam files are saved in multiple different directories and I'm wondering if there is a way to input multiple bam files instead of a directory which contains all the bam files. Best, Hyunji -- Dr Hyun Ji Noh Postdoctoral Associate Broad Institute of MIT and Harvard 5 Cambridge Center (Room 1316A) Cambridge, MA 02142 USA Phone: +1(617)714-7863 Email: no...@br... |
From: David R. <ri...@ce...> - 2013-05-27 06:51:19
|
Hello, I wanted to ask this question again. SNVer doesn't find any SNPs, althoug when I look at the mapped data, I clearly see them. In the error.txt file it says [Indel significant], but from the mapped reads there is no indel. Please tell me if you need more information. Best regards, David On 04/11/2013 02:11 AM, Wei Wang wrote: > Hi David, > > Could you provide an example? or a sample vcf? > This may be helpful for debugging. > > Thanks, > Wei > > > On Wed, Apr 10, 2013 at 8:36 AM, David Ries > <ri...@ce... <mailto:ri...@ce...>> > wrote: > > Hi, > > I used SNVer to call variants for two pools of 180 individuals, with a > coverage of about 60x. > I get a filtered indel file which is as expected, i.e. there are > indels > with AF between 0.1 and 1.0 and reasonable coverage. > > But for the SNP file, there are only (!) SNPs with AF = 0 in > either one > of the Pools. What could be the reason for this, and why are SNPs/ > alternative Alleles called, when there are no reads indicating > a SNP? > > > Best regards, > > David > > > -- > David Ries > Bielefeld University, Department of Biology > Genome Research / Lehrstuhl fuer Genomforschung > Universitaetsstrasse 25 > 33615 Bielefeld > Germany > > Office: V6-142 > Tel.: +49-521-106-2639 <tel:%2B49-521-106-2639> > > > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for > building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free > account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > Snver-help mailing list > Snv...@li... > <mailto:Snv...@li...> > https://lists.sourceforge.net/lists/listinfo/snver-help > > > > > -- > Wei |
From: David R. <ri...@ce...> - 2013-04-29 13:24:57
|
Hi, could it be a problem, that the coverage is lower than the number of pooled individuals? Best regards, David On 04/11/13 02:11, Wei Wang wrote: > Hi David, > > Could you provide an example? or a sample vcf? > This may be helpful for debugging. > > Thanks, > Wei > > > On Wed, Apr 10, 2013 at 8:36 AM, David Ries <ri...@ce... > <mailto:ri...@ce...>> wrote: > > Hi, > > I used SNVer to call variants for two pools of 180 individuals, with a > coverage of about 60x. > I get a filtered indel file which is as expected, i.e. there are indels > with AF between 0.1 and 1.0 and reasonable coverage. > > But for the SNP file, there are only (!) SNPs with AF = 0 in either one > of the Pools. What could be the reason for this, and why are SNPs/ > alternative Alleles called, when there are no reads indicating > a SNP? > > > Best regards, > > David > > > -- > David Ries > Bielefeld University, Department of Biology > Genome Research / Lehrstuhl fuer Genomforschung > Universitaetsstrasse 25 > 33615 Bielefeld > Germany > > Office: V6-142 > Tel.: +49-521-106-2639 <tel:%2B49-521-106-2639> > > > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > Snver-help mailing list > Snv...@li... <mailto:Snv...@li...> > https://lists.sourceforge.net/lists/listinfo/snver-help > > > > > -- > Wei -- David Ries Bielefeld University, Department of Biology Genome Research / Lehrstuhl fuer Genomforschung Universitaetsstrasse 25 33615 Bielefeld Germany Office: V6-142 Tel.: +49-521-106-2639 |
From: David R. <ri...@ce...> - 2013-04-12 11:31:55
|
Hi Wei, I sent you a sample of the vcf. Because they tend to be big, I filtered it for covered SNPs. lcl|Chr1 57282 . t g . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:2 0:1 lcl|Chr1 57291 . t c . PASS DP=11;AF=0.000;NP=2;PV=1.0 AC:DP 0:10 0:1 lcl|Chr1 81336 . c a . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:4 lcl|Chr1 107135 . g c . PASS DP=6;AF=0.000;NP=2;PV=1.0 AC:DP 0:5 0:1 lcl|Chr1 115858 . t a . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:2 0:1 lcl|Chr1 118158 . a n . PASS DP=2;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:1 lcl|Chr1 145227 . t c . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:2 0:1 lcl|Chr1 145986 . n t . PASS DP=2;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:1 lcl|Chr1 146568 . t g . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:4 0:1 lcl|Chr1 178413 . n g . PASS DP=2;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:1 lcl|Chr1 203358 . t n . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:4 lcl|Chr1 254451 . t g . PASS DP=2;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:1 lcl|Chr1 265123 . a c . PASS DP=4;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:3 lcl|Chr1 266002 . t g . PASS DP=7;AF=0.000;NP=2;PV=1.0 AC:DP 0:6 0:1 lcl|Chr1 285173 . a t . PASS DP=4;AF=0.000;NP=2;PV=1.0 AC:DP 0:3 0:1 lcl|Chr1 291661 . g a . PASS DP=9;AF=0.000;NP=2;PV=1.0 AC:DP 0:8 0:1 lcl|Chr1 293286 . n t . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:2 0:1 lcl|Chr1 295363 . t c . PASS DP=15;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:14 lcl|Chr1 369925 . t a . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:2 0:1 lcl|Chr1 376647 . t g . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:4 0:1 lcl|Chr1 376835 . a g . PASS DP=3;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:2 lcl|Chr1 398309 . n t . PASS DP=7;AF=0.000;NP=2;PV=1.0 AC:DP 0:6 0:1 lcl|Chr1 426015 . a n . PASS DP=28;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:27 lcl|Chr1 484452 . c t . PASS DP=2;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:1 lcl|Chr1 518565 . g c . PASS DP=4;AF=0.000;NP=2;PV=1.0 AC:DP 0:3 0:1 lcl|Chr1 519657 . a n . PASS DP=4;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:3 lcl|Chr1 547977 . n a . PASS DP=16;AF=0.000;NP=2;PV=1.0 AC:DP 0:15 0:1 lcl|Chr1 562502 . t n . PASS DP=18;AF=0.000;NP=2;PV=1.0 AC:DP 0:5 0:13 lcl|Chr1 623683 . g t . PASS DP=11;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:10 lcl|Chr1 644223 . c a . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:1 0:4 lcl|Chr1 663038 . g n . PASS DP=5;AF=0.000;NP=2;PV=1.0 AC:DP 0:3 0:2 Best, David On 04/11/13 02:11, Wei Wang wrote: > Hi David, > > Could you provide an example? or a sample vcf? > This may be helpful for debugging. > > Thanks, > Wei > > > On Wed, Apr 10, 2013 at 8:36 AM, David Ries <ri...@ce... > <mailto:ri...@ce...>> wrote: > > Hi, > > I used SNVer to call variants for two pools of 180 individuals, with a > coverage of about 60x. > I get a filtered indel file which is as expected, i.e. there are indels > with AF between 0.1 and 1.0 and reasonable coverage. > > But for the SNP file, there are only (!) SNPs with AF = 0 in either one > of the Pools. What could be the reason for this, and why are SNPs/ > alternative Alleles called, when there are no reads indicating > a SNP? > > > Best regards, > > David > > > -- > David Ries > Bielefeld University, Department of Biology > Genome Research / Lehrstuhl fuer Genomforschung > Universitaetsstrasse 25 > 33615 Bielefeld > Germany > > Office: V6-142 > Tel.: +49-521-106-2639 <tel:%2B49-521-106-2639> > > > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > Snver-help mailing list > Snv...@li... <mailto:Snv...@li...> > https://lists.sourceforge.net/lists/listinfo/snver-help > > > > > -- > Wei -- David Ries Bielefeld University, Department of Biology Genome Research / Lehrstuhl fuer Genomforschung Universitaetsstrasse 25 33615 Bielefeld Germany Office: V6-142 Tel.: +49-521-106-2639 |
From: Wei W. <ww...@us...> - 2013-04-11 00:11:54
|
Hi David, Could you provide an example? or a sample vcf? This may be helpful for debugging. Thanks, Wei On Wed, Apr 10, 2013 at 8:36 AM, David Ries <ri...@ce...>wrote: > Hi, > > I used SNVer to call variants for two pools of 180 individuals, with a > coverage of about 60x. > I get a filtered indel file which is as expected, i.e. there are indels > with AF between 0.1 and 1.0 and reasonable coverage. > > But for the SNP file, there are only (!) SNPs with AF = 0 in either one > of the Pools. What could be the reason for this, and why are SNPs/ > alternative Alleles called, when there are no reads indicating > a SNP? > > > Best regards, > > David > > > -- > David Ries > Bielefeld University, Department of Biology > Genome Research / Lehrstuhl fuer Genomforschung > Universitaetsstrasse 25 > 33615 Bielefeld > Germany > > Office: V6-142 > Tel.: +49-521-106-2639 > > > > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help > -- Wei |
From: Wei W. <ww...@us...> - 2013-04-11 00:09:33
|
Hi Marty, Frankly speaking, our maintainer has graduated and we have been looking for a new maintainer. I may not have time to take it over until this summer. Sorry for any inconvenience, Wei On Wed, Apr 10, 2013 at 1:51 PM, Marty Kardos <mar...@gm...> wrote: > Hello Wei; > > Has the problem raised by James Kijas below (October 21, 2012) been resolved (incorrect calculation of the alternative allele frequency for pooled NGS data)? Thanks very much. > > Marty Kardos > > Hi James, > > I agree with you. It makes more sense that DP=18 in such case you mentioned. > We will look into and fix this problem. Thanks for your comment. > > Wei > > On Sun, Oct 21, 2012 at 11:14 PM, <James.Kijas@...> wrote: > > Hi SNVer users, > > > > > > > > I am using SNVer to call variants in pooled NGS sequence. As background, we > > pooled DNA from ten individuals into a single tube, before sequencing to > > around 15 fold mapped read coverage. We mapped the Illumina reads using BWA > > to create the .bam files that serve as input for SNVer. > > > > > > > > My question concerns how SNVer calculates the alternate allele frequency > > (AF). To illustrate my question, consider a nucleotide that is covered by 20 > > reads have each have mapping quality score > 20. In 18 of these reads, the > > alternate base is present with a base quality > 17. In the remaining 2 > > reads, the alternate base is present with base quality < 17. The total depth > > (DP) is recorded as 20, the alternate allele count (AC) is recorded as 18 > > and the alternative allele frequency (AF) is 18/20 = 0.9. For many of these > > cases, the true AF equals 1.0. > > > > > > > > What I would like to do it get SNVer to ignore counting to 2 reads (with > > high mapping quality) at the positions with low base quality. Does anyone > > have a suggestion about how to do this? If this explanation doesn’t make > > sense, please let me know > > > > > > > > Any help appreciated > > > > > > > > Cheers, James > > > > > > > > > > > > > > > > From: Kijas, James (CAFHS, St. Lucia) > > Sent: Monday, 22 October 2012 3:54 PM > > To: 'Snver-help@...' > > Subject: > > > > > > > > > > > > > > > > James Kijas > > > -- > Marty Kardos > PhD candidate > Montana Conservation Genetics Lab > NSF Montana Ecology of Infectious Disease IGERT trainee > Graduate Fellow of the Montana Institute on Ecosystems > University of Montana > > > > > ------------------------------------------------------------------------------ > Precog is a next-generation analytics platform capable of advanced > analytics on semi-structured data. The platform includes APIs for building > apps and a phenomenal toolset for data science. Developers can use > our toolset for easy data analysis & visualization. Get a free account! > http://www2.precog.com/precogplatform/slashdotnewsletter > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help > > -- Wei |
From: Marty K. <mar...@gm...> - 2013-04-10 17:51:46
|
Hello Wei; Has the problem raised by James Kijas below (October 21, 2012) been resolved (incorrect calculation of the alternative allele frequency for pooled NGS data)? Thanks very much. Marty Kardos Hi James, I agree with you. It makes more sense that DP=18 in such case you mentioned. We will look into and fix this problem. Thanks for your comment. Wei On Sun, Oct 21, 2012 at 11:14 PM, <James.Kijas@...> wrote: > Hi SNVer users, > > > > I am using SNVer to call variants in pooled NGS sequence. As background, we > pooled DNA from ten individuals into a single tube, before sequencing to > around 15 fold mapped read coverage. We mapped the Illumina reads using BWA > to create the .bam files that serve as input for SNVer. > > > > My question concerns how SNVer calculates the alternate allele frequency > (AF). To illustrate my question, consider a nucleotide that is covered by 20 > reads have each have mapping quality score > 20. In 18 of these reads, the > alternate base is present with a base quality > 17. In the remaining 2 > reads, the alternate base is present with base quality < 17. The total depth > (DP) is recorded as 20, the alternate allele count (AC) is recorded as 18 > and the alternative allele frequency (AF) is 18/20 = 0.9. For many of these > cases, the true AF equals 1.0. > > > > What I would like to do it get SNVer to ignore counting to 2 reads (with > high mapping quality) at the positions with low base quality. Does anyone > have a suggestion about how to do this? If this explanation doesn’t make > sense, please let me know > > > > Any help appreciated > > > > Cheers, James > > > > > > > > From: Kijas, James (CAFHS, St. Lucia) > Sent: Monday, 22 October 2012 3:54 PM > To: 'Snver-help@...' > Subject: > > > > > > > > James Kijas -- Marty Kardos PhD candidate Montana Conservation Genetics Lab NSF Montana Ecology of Infectious Disease IGERT trainee Graduate Fellow of the Montana Institute on Ecosystems University of Montana |
From: David R. <ri...@ce...> - 2013-04-10 12:56:12
|
Hi, I used SNVer to call variants for two pools of 180 individuals, with a coverage of about 60x. I get a filtered indel file which is as expected, i.e. there are indels with AF between 0.1 and 1.0 and reasonable coverage. But for the SNP file, there are only (!) SNPs with AF = 0 in either one of the Pools. What could be the reason for this, and why are SNPs/ alternative Alleles called, when there are no reads indicating a SNP? Best regards, David -- David Ries Bielefeld University, Department of Biology Genome Research / Lehrstuhl fuer Genomforschung Universitaetsstrasse 25 33615 Bielefeld Germany Office: V6-142 Tel.: +49-521-106-2639 |
From: Wei W. <ww...@us...> - 2013-03-14 00:10:45
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Hi Earl, Sorry to get you back late. Below are my comments: On Fri, Mar 8, 2013 at 7:48 PM, earl middlebrook <eam...@gm...> wrote: > Hi, > > There are two issues that i hope someone else has seen, and have a > relatively painless fix. > > The first. > In all my SNVer *.vcfs i get some proportion of calls that have a PV= 1.7 > E308 and the AC:DP values > are lacking. These account for about 1 in 20 loci. The failed log shows > that these loci fail because of [Indel Significant], ironically there are no > significant indels called. We originally do not consider a position as SNP if the alternative count is smaller than indel count. The "Indel Significant" here just means SNVer observes more indel count than alt count. The significance of indel calls are still based on p-values. Sorry for any misleading. > The second. > I have a pipeline that works well for one data set, with the exception of > the above issue, but when another dataset is used, from the same sequencer, > as input, it doesnt show any variation in the sample.raw.vcf file (AC:DP > bellow). I have used GATK unifiedGenotyper and samtools/bcftools to call > SNVs from the same data set and get 8 SNVs that are approx. 100% of the > population. I have a feeling all the variation is getting thrown out due to > mapping quality incompatibility. > > FMuLV_amp_trim 207 . c c . PASS > DP=4146;AF=0.000;NP=1;PV=1.0 AC:DP 0:4146 > FMuLV_amp_trim 208 . a . . FAILED > DP=4041;AF=NaN;NP=0;PV=1.7976931348623157E308 AC:DP NA:NA > FMuLV_amp_trim 209 . c c . PASS > DP=4109;AF=0.000;NP=1;PV=1.0 AC:DP 0:4109 > FMuLV_amp_trim 210 . c c . PASS > DP=4092;AF=0.000;NP=1;PV=1.0 AC:DP 0:4092 > FMuLV_amp_trim 211 . c c . PASS > DP=4309;AF=0.000;NP=1;PV=1.0 AC:DP 0:4309 > FMuLV_amp_trim 212 . c c . PASS > DP=4419;AF=0.000;NP=1;PV=1.0 AC:DP 0:4419 > FMuLV_amp_trim 213 . c c . PASS > DP=4987;AF=0.000;NP=1;PV=1.0 AC:DP 0:4987 > FMuLV_amp_trim 214 . c . . FAILED > DP=4991;AF=NaN;NP=0;PV=1.7976931348623157E308 > AC:DP NA:NA > FMuLV_amp_trim 215 . t t . PASS > DP=5007;AF=0.000;NP=1;PV=1.0 AC:DP 0:5007 > FMuLV_amp_trim 216 . t t . PASS > DP=5027;AF=0.000;NP=1;PV=1.0 AC:DP 0:5027 > FMuLV_amp_trim 217 . a a . PASS > DP=5013;AF=0.000;NP=1;PV=1.0 AC:DP 0:5013 > Is it possible to lower -mq and/or -bq to see if the alternative allele could be included? Thanks, Wei > > I am sorry if this is something dumb like a mapping or base qual score. The > reads are from an illumina MySeq with Bowtie2:alignment, Samtools:sam->bam > sort and rmdup, and then SNVer calls. > > Thanks in advance, > Earl > > > ------------------------------------------------------------------------------ > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help > -- Wei |
From: Wei W. <ww...@us...> - 2013-03-13 23:55:23
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Hi Shelbi, Sorry to get you back late. It seems that the mapped position may be out of reference boundary when piling up the reads. Is it possible some mapped reads are outside the reference genome? Thanks, Wei On Tue, Mar 5, 2013 at 5:34 PM, Russell, Shelbi <she...@fa...> wrote: > Hi, > > I am having trouble getting SNVer to finish running on one of my datasets. I had no problem generating the filtered and raw vcf files for my smaller dataset (about 2 million reads). However, SNVer seems to have an error at the pileup step for my larger dataset (205 million reads). I have pasted the report below. I tried reindexing the files in case there was a problem there, but I got the same error. Do you have any idea what the problem is? > > Thanks for your time. > > Shelbi > > > Your job looked like: > > ------------------------------------------------------------ > # LSBATCH: User input > java -jar SNVerPool.jar -i /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned/ -r /n/nobackup2/cavanaugh/shelbirussell/alignments/reference/Solemya_velum_sym_genome_all_scaffolds.fasta -c Sv_sym_pool_info -o All_Sv_sym_SNVer -p 0.1 -a 2 -t 0.05 > ------------------------------------------------------------ > > Successfully completed. > > Resource usage summary: > > CPU time : 1868.72 sec. > Max Memory : 2312 MB > Max Swap : 6409 MB > > Max Processes : 3 > Max Threads : 21 > > The output (if any) follows: > > Input bam directory is : /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned/ > Output result file is : All_Sv_sym_SNVer.raw.vcf, All_Sv_sym_SNVer.indel.raw.vcf > > Collecting total number of reads... > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//KB16gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//Unamp_KB18gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//PJRI36gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//PJRI37gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//PJRI38gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//PJRI39gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//SRI2gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//SRI3gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//Unamp_PJRI53gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//Unamp_SB7gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//SB8gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//Unamp_DML1gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > /n/nobackup2/cavanaugh/shelbirussell/alignments/realigned//DML2gill_realigned.bam:HAPLOIDS[50]MQ[20]BQ[17] > > Ready for pileup... > Progress: 0%===3793java.lang.ArrayIndexOutOfBoundsException: 3793 > at net.sf.snver.pileup.meta.PileupPool.getRef(PileupPool.java:203) > at net.sf.snver.pileup.meta.PileupPool.compute(PileupPool.java:67) > at net.sf.snver.pileup.loader.Peeker.next(Peeker.java:267) > at net.sf.snver.pileup.SNVerPool._pileup(SNVerPool.java:203) > at net.sf.snver.pileup.SNVerPool.pileup(SNVerPool.java:62) > at net.sf.snver.pileup.SNVerPool.main(SNVerPool.java:56) > > > > > > ------------------------------------------------------------------------------ > Symantec Endpoint Protection 12 positioned as A LEADER in The Forrester > Wave(TM): Endpoint Security, Q1 2013 and "remains a good choice" in the > endpoint security space. For insight on selecting the right partner to > tackle endpoint security challenges, access the full report. > http://p.sf.net/sfu/symantec-dev2dev > _______________________________________________ > Snver-help mailing list > Snv...@li... > https://lists.sourceforge.net/lists/listinfo/snver-help -- Wei |