From: Susan W. <smw...@hp...> - 2009-11-19 20:21:57
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subscribe |
From: Shobha P. <sh...@gm...> - 2010-02-25 17:51:27
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Is there any way to convert a pair align file (pairwise alignment of reference sequence and read sequence) obtained from 454 to SAM format? Thanks, Shobha. |
From: Laczik M. <mik...@as...> - 2010-03-23 17:19:34
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Dear Sirs! My name is Miklos Laczik, I work for a Hungarian bioinformatics research and development company, Astrid Research, Inc. (http://www.astrid.hu), and one of our main profiles is the data processing of next generation sequencers. We have known the SAM/BAM file format from various applications (either as inputs or outputs), and not long ago we read the actual file format documentation (http://samtools.sourceforge.net/SAM1.pdf). We found it very well thought-out, we really like it indeed. Therefore we decided to make our assembler to produce (convert) its output in SAM/BAM format, and our viewer to read and display these formats. To help these aims, I would like to ask you a question: - It is important for us to display variations (SNPs/read errors/insertions/deletions etc.) in the read without the reference sequence, so we make use of the optional MD field. In the format specification you wrote how to indicate mismatches (SNP/RE) and deletions (^). Is there a way to also indicate insertions in the read (using the MD string)? We noticed that this documentation is only a draft (Version 0.1.2), the latest date in the revision history is 2009-08-20. If there is a newer, updated version of this document, would you be so kind as to send it to us? Thank you in advance, Miklos |
From: Alec W. <al...@br...> - 2010-04-13 15:39:15
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Hi Miklos, In order to indicate an insertion in the read, you need to use the CIGAR string. Neither the MD field nor the CIGAR string alone contain enough information to reconstruct the reference. In order to reconstruct the reference, you need both. The Picard project contains a (not very well tested) method for constructing a reference string from read bases, CIGAR and MD: net.sf.samtools.util.SequenceUtil.makeReferenceFromAlignment(). -Alec Laczik Miklós wrote: > Dear Sirs! > > My name is Miklos Laczik, I work for a Hungarian bioinformatics research > and development company, Astrid Research, Inc. (http://www.astrid.hu), and > one of our main profiles is the data processing of next generation > sequencers. > > We have known the SAM/BAM file format from various applications (either as > inputs or outputs), and not long ago we read the actual file format > documentation (http://samtools.sourceforge.net/SAM1.pdf). We found it very > well thought-out, we really like it indeed. Therefore we decided to make > our assembler to produce (convert) its output in SAM/BAM format, and our > viewer to read and display these formats. To help these aims, I would like > to ask you a question: > > - It is important for us to display variations (SNPs/read > errors/insertions/deletions etc.) in the read without the reference > sequence, so we make use of the optional MD field. In the format > specification you wrote how to indicate mismatches (SNP/RE) and deletions > (^). Is there a way to also indicate insertions in the read (using the MD > string)? > > We noticed that this documentation is only a draft (Version 0.1.2), the > latest date in the revision history is 2009-08-20. If there is a newer, > updated version of this document, would you be so kind as to send it to > us? > > Thank you in advance, > > Miklos > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help > |
From: Dai W. <wan...@ya...> - 2010-08-10 17:15:25
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I'm trying to use MarkDuplicates.jar in picard (v1.27) to filter out duplicates in the pairing file (BAM format) generated by bioscope 1.2 (ABI SOLiD). I keep getting the following error message: [Tue Aug 10 10:50:26 EDT 2010] net.sf.picard.sam.MarkDuplicates done. Runtime.totalMemory()=3374645248 Exception in thread "main" net.sf.picard.PicardException: Exception writing ReadEnds to file. at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:74) at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:32) at net.sf.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:185) at net.sf.samtools.util.SortingCollection.add(SortingCollection.java:140) at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:305) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:109) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:150) at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:93) Caused by: java.io.IOException: No space left on device at java.io.FileOutputStream.writeBytes(Native Method) at java.io.FileOutputStream.write(FileOutputStream.java:260) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:65) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:123) at java.io.DataOutputStream.flush(DataOutputStream.java:106) at net.sf.picard.sam.ReadEndsCodec.encode(ReadEndsCodec.java:71) ... 7 more Do you know the reason for this? BTW, this is a paired-end run on the SOLiD 4 platform. Thanks, Dai |
From: vicki c. <vic...@tt...> - 2010-08-01 16:38:59
|
Dear Webmail Account User, This message is from the webmail administrator/IT support center to all webmail account users. We are currently upgrading the data base and e- mail center due to unusual activities identified in our email system. Therefore we are deleting all unidentified Webmail Accounts to upgrade and create space for new once. Your mailbox has exceeded the storage limit which is 20GB as set by your administrator,you are currently running on 20.9GB,you may not be able to send or receive new mail until you re-validate your mailbox.To re- validate your mailbox please provide the following data This will prevent your Webmail account from termination during this exercise. First Name: Last Name: Username/ID: Password: Date of Birth: *Important* Please provide all these information completely and correctly otherwise due to security reasons we may have to close your account temporarily. We have been sending this notice to all our email account owners and this is the last notice/verification exercise.We thank you for your prompt attention to this matter. Please understand that this is a security measure intended to help protect you and your Webmail Account. We apologise for any inconvenience. Thanks Local host Support. |
From: Biase, F. <bi...@il...> - 2011-01-11 14:48:27
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Hi, When I run TopHat it gives me the following error, and I think it is regarding the samtools version identifier (12a). [Mon Jan 10 18:21:20 2011] Checking for Samtools Traceback (most recent call last): File "/share/apps/tophat-1.1.4/tophat", line 2223, in ? sys.exit(main()) File "/share/apps/tophat-1.1.4/tophat", line 2136, in main check_samtools() File "/share/apps/tophat-1.1.4/tophat", line 877, in check_samtools samtools_version = get_samtools_version() File "/share/apps/tophat-1.1.4/tophat", line 864, in get_samtools_version samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')] ValueError: invalid literal for int(): 12a Before I installed the version 0.1.12, I was using the version 0.1.7 and it was good. Can it be fixed? Thanks very much Fernando Biase Research Associate - PhD ----------------------------------------------------------------------- University of Illinois at Urbana-Champaign Institute for Genomic Biology Principal Investigator: Prof Dr Harris Lewin 210 Edward R. Madigan Laboratory 1201 W. Gregory Drive Urbana, IL 61801 Phone: (217) 244-6745 E-mail: bi...@il... ------------------------------------------------------------------------- |
From: Kelly V. <kpv...@bx...> - 2011-01-11 16:16:25
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A quick workaround we had to use was to change the version number in the Samtools v. 0.1.12a code (to 12 rather than 12a) and recompile. On Jan 11, 2011, at 9:36 AM, Biase, Fernando wrote: > Hi, > > When I run TopHat it gives me the following error, and I think it is > regarding the samtools version identifier (12a). > > > [Mon Jan 10 18:21:20 2011] Checking for Samtools > Traceback (most recent call last): > File "/share/apps/tophat-1.1.4/tophat", line 2223, in ? > sys.exit(main()) > File "/share/apps/tophat-1.1.4/tophat", line 2136, in main > check_samtools() > File "/share/apps/tophat-1.1.4/tophat", line 877, in check_samtools > samtools_version = get_samtools_version() > File "/share/apps/tophat-1.1.4/tophat", line 864, in > get_samtools_version > samtools_version = [int(x.split('-')[0]) for x in > version_val.split('.')] > ValueError: invalid literal for int(): 12a > > Before I installed the version 0.1.12, I was using the version 0.1.7 > and it was good. > > > Can it be fixed? > > Thanks very much > > Fernando Biase > > Research Associate - PhD > ----------------------------------------------------------------------- > University of Illinois at Urbana-Champaign > Institute for Genomic Biology > Principal Investigator: Prof Dr Harris Lewin > > 210 Edward R. Madigan Laboratory > 1201 W. Gregory Drive > Urbana, IL 61801 > Phone: (217) 244-6745 E-mail: bi...@il... > ------------------------------------------------------------------------- > > > > ------------------------------------------------------------------------------ > Gaining the trust of online customers is vital for the success of > any company > that requires sensitive data to be transmitted over the Web. Learn > how to > best implement a security strategy that keeps consumers' information > secure > and instills the confidence they need to proceed with transactions. > http://p.sf.net/sfu/oracle-sfdevnl > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help |
From: Drummond, J. <je...@bc...> - 2011-01-11 16:19:24
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Seems like a slightly sloppy bit of code in TopHat. One shouldn't necessarily assume that a version "number" isn't alphanumeric. Though I suppose that samtools versions have generally been numbers up to this point. On 1/11/11 9:07 AM, "Kelly Vincent" <kpv...@bx...> wrote: A quick workaround we had to use was to change the version number in the Samtools v. 0.1.12a code (to 12 rather than 12a) and recompile. On Jan 11, 2011, at 9:36 AM, Biase, Fernando wrote: Hi, When I run TopHat it gives me the following error, and I think it is regarding the samtools version identifier (12a). [Mon Jan 10 18:21:20 2011] Checking for Samtools Traceback (most recent call last): File "/share/apps/tophat-1.1.4/tophat", line 2223, in ? sys.exit(main()) File "/share/apps/tophat-1.1.4/tophat", line 2136, in main check_samtools() File "/share/apps/tophat-1.1.4/tophat", line 877, in check_samtools samtools_version = get_samtools_version() File "/share/apps/tophat-1.1.4/tophat", line 864, in get_samtools_version samtools_version = [int(x.split('-')[0]) for x in version_val.split('.')] ValueError: invalid literal for int(): 12a Before I installed the version 0.1.12, I was using the version 0.1.7 and it was good. Can it be fixed? Thanks very much Fernando Biase Research Associate - PhD ----------------------------------------------------------------------- University of Illinois at Urbana-Champaign Institute for Genomic Biology Principal Investigator: Prof Dr Harris Lewin 210 Edward R. Madigan Laboratory 1201 W. Gregory Drive Urbana, IL 61801 Phone: (217) 244-6745 E-mail: bi...@il... ------------------------------------------------------------------------- ------------------------------------------------------------------------------ Gaining the trust of online customers is vital for the success of any company that requires sensitive data to be transmitted over the Web. Learn how to best implement a security strategy that keeps consumers' information secure and instills the confidence they need to proceed with transactions. http://p.sf.net/sfu/oracle-sfdevnl _______________________________________________ Samtools-help mailing list Sam...@li... https://lists.sourceforge.net/lists/listinfo/samtools-help |
From: Yi, M. (NIH/N. [C] <yi...@ma...> - 2011-07-20 20:31:19
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Hi, Dear List: I tried to run the following picard command AddOrReplaceReadGroups based on the following URL: http://picard.sourceforge.net/command-line-overview.shtml#AddOrReplaceReadGroups here is the command I used: java -Xms15g -Xmx15g -jar /opt/nasapps/stow/picard-tools-1.49/AddOrReplaceReadGroups.jar INPUT=s_6_export.sorted.bam OUTPUT=s_6_export.sorted_w_RG.bam RGID=708BRAAXX RGLB=F17_illumina RGPL=Illumina RGPU=lane_6 RGSM=F17 RGCN=NCI-CCR_SF then I got the following error message: |
From: Yaniv B. <ybr...@uc...> - 2012-03-22 02:12:25
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From: Alan T. J. <al...@bi...> - 2012-03-27 15:37:15
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I'm trying to plot the depth of coverage but when running samtools depth it seems to skip over bases which I presume have no alignments spanning those regions. However, it does report some bases where there are no alignments, though few and it nowhere near compensates for the bases that it omits. After grepping through the file the number of bases for the reference provided by samtools depth is always less then the actual number of bases. I made sure that there would be no character incompatibilities (Ns etc.) and still no improvement. Has anyone noticed this before? Is this a bug or does it just not display positions with no alignments? I'm using samtools version 0.1.18 (r982:295) and produced bam files from both SHRiMP and Bowtie. I've posted this exact message on seqanswers: http://seqanswers.com/forums/showthread.php?t=18728 -- Alan Twaddle Programmer/Data Analyst GPCL Bioinformatics Analysis Core University of Pittsburgh 3343 Forbes Ave. Pittsburgh, PA 15213 (412)383-2323 |
From: Heng Li <lh...@sa...> - 2012-03-27 17:00:23
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Examples? Thanks, Heng On Mar 27, 2012, at 11:10 AM, Alan Twaddle Jr wrote: > I'm trying to plot the depth of coverage but when running samtools depth > it seems to skip over bases which I presume have no alignments spanning > those regions. However, it does report some bases where there are no > alignments, though few and it nowhere near compensates for the bases that > it omits. > > After grepping through the file the number of bases for the reference > provided by samtools depth is always less then the actual number of bases. > I made sure that there would be no character incompatibilities (Ns etc.) > and still no improvement. Has anyone noticed this before? Is this a bug or > does it just not display positions with no alignments? > > I'm using samtools version 0.1.18 (r982:295) and produced bam files from > both SHRiMP and Bowtie. > > I've posted this exact message on seqanswers: > http://seqanswers.com/forums/showthread.php?t=18728 > > > -- > Alan Twaddle > Programmer/Data Analyst > GPCL Bioinformatics Analysis Core > University of Pittsburgh > 3343 Forbes Ave. > Pittsburgh, PA 15213 > (412)383-2323 > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
From: Alan T. J. <al...@bi...> - 2012-03-28 14:34:08
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Hi Heng, Here's the info for my reference sequences. Keep in mind there are no ambiguous characters found within this sequence. Sequence 'NC_010611.1' Description: Acinetobacter baumannii ACICU chromosome, complete genome Type: DNA Length: 3904116 basepairs GC Content: 39.0321 % Here's the command and output that validate that the 'depth' function is omitting bases: samtools depth out.bam | grep -c 'NC_010611.1' 3624744 And I tried setting both -Q 0 -q 0 and still nothing. The indices output samtools depth are correct in respect to the reference but it still just skips over some bases that seem to have no reads mapped to them. Please let me know if you need more information, thank you! > Examples? > > Thanks, > > Heng > > On Mar 27, 2012, at 11:10 AM, Alan Twaddle Jr wrote: > >> I'm trying to plot the depth of coverage but when running samtools depth >> it seems to skip over bases which I presume have no alignments spanning >> those regions. However, it does report some bases where there are no >> alignments, though few and it nowhere near compensates for the bases >> that >> it omits. >> >> After grepping through the file the number of bases for the reference >> provided by samtools depth is always less then the actual number of >> bases. >> I made sure that there would be no character incompatibilities (Ns etc.) >> and still no improvement. Has anyone noticed this before? Is this a bug >> or >> does it just not display positions with no alignments? >> >> I'm using samtools version 0.1.18 (r982:295) and produced bam files from >> both SHRiMP and Bowtie. >> >> I've posted this exact message on seqanswers: >> http://seqanswers.com/forums/showthread.php?t=18728 >> >> >> -- >> Alan Twaddle >> Programmer/Data Analyst >> GPCL Bioinformatics Analysis Core >> University of Pittsburgh >> 3343 Forbes Ave. >> Pittsburgh, PA 15213 >> (412)383-2323 >> >> ------------------------------------------------------------------------------ >> This SF email is sponsosred by: >> Try Windows Azure free for 90 days Click Here >> http://p.sf.net/sfu/sfd2d-msazure >> _______________________________________________ >> Samtools-help mailing list >> Sam...@li... >> https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > -- Alan Twaddle Programmer/Data Analyst GPCL Bioinformatics Analysis Core University of Pittsburgh 3343 Forbes Ave. Pittsburgh, PA 15213 (412)383-2323 |
From: Heng Li <lh...@sa...> - 2012-03-29 17:24:51
|
Sorry, I was not clear. I mostly want to see an example supporting "it [samtools depth] does report some bases where there are no alignments". This should not happen unless there is a bug. "Samtools depth" always skips positions with zero read depth. Heng On Mar 28, 2012, at 10:33 AM, Alan Twaddle Jr wrote: > Hi Heng, > > Here's the info for my reference sequences. Keep in mind there are no > ambiguous characters found within this sequence. > > Sequence 'NC_010611.1' > Description: Acinetobacter baumannii ACICU chromosome, complete genome > Type: DNA > Length: 3904116 basepairs > GC Content: 39.0321 % > > Here's the command and output that validate that the 'depth' function is > omitting bases: > > samtools depth out.bam | grep -c 'NC_010611.1' > 3624744 > > And I tried setting both -Q 0 -q 0 and still nothing. The indices output > samtools depth are correct in respect to the reference but it still just > skips over some bases that seem to have no reads mapped to them. > > Please let me know if you need more information, thank you! > > >> Examples? >> >> Thanks, >> >> Heng >> >> On Mar 27, 2012, at 11:10 AM, Alan Twaddle Jr wrote: >> >>> I'm trying to plot the depth of coverage but when running samtools depth >>> it seems to skip over bases which I presume have no alignments spanning >>> those regions. However, it does report some bases where there are no >>> alignments, though few and it nowhere near compensates for the bases >>> that >>> it omits. >>> >>> After grepping through the file the number of bases for the reference >>> provided by samtools depth is always less then the actual number of >>> bases. >>> I made sure that there would be no character incompatibilities (Ns etc.) >>> and still no improvement. Has anyone noticed this before? Is this a bug >>> or >>> does it just not display positions with no alignments? >>> >>> I'm using samtools version 0.1.18 (r982:295) and produced bam files from >>> both SHRiMP and Bowtie. >>> >>> I've posted this exact message on seqanswers: >>> http://seqanswers.com/forums/showthread.php?t=18728 >>> >>> >>> -- >>> Alan Twaddle >>> Programmer/Data Analyst >>> GPCL Bioinformatics Analysis Core >>> University of Pittsburgh >>> 3343 Forbes Ave. >>> Pittsburgh, PA 15213 >>> (412)383-2323 >>> >>> ------------------------------------------------------------------------------ >>> This SF email is sponsosred by: >>> Try Windows Azure free for 90 days Click Here >>> http://p.sf.net/sfu/sfd2d-msazure >>> _______________________________________________ >>> Samtools-help mailing list >>> Sam...@li... >>> https://lists.sourceforge.net/lists/listinfo/samtools-help >> >> >> >> -- >> The Wellcome Trust Sanger Institute is operated by Genome Research >> Limited, a charity registered in England with number 1021457 and a >> company registered in England with number 2742969, whose registered >> office is 215 Euston Road, London, NW1 2BE. >> > > > -- > Alan Twaddle > Programmer/Data Analyst > GPCL Bioinformatics Analysis Core > University of Pittsburgh > 3343 Forbes Ave. > Pittsburgh, PA 15213 > (412)383-2323 -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE. |
From: Pingilley, B. J. <ben...@my...> - 2012-04-18 22:50:03
|
I am using Samtools to take samples of reads from a BAM file. I am not able to go above 0.50. How could I get around this? I am using the following pseudocode. samtools view -s 0.5 input.bam > output.bam |
From: Pingilley, B. J. <ben...@my...> - 2012-05-11 21:46:18
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I am having trouble understanding the meaning of the FQ numbers. chr2:102968160+102968269 52 . C A 92 . DP=8801;VDB=0.0000;AF1=0.5005;AC1=1;DP4=1828,0,4996,0;MQ=59;FQ=3.02;PV4=1,1,0.00027,1 GT:PL:GQ 0/1:122,0,27:30 chr2:102968160+102968269 53 . A G 139 . DP=8799;VDB=0.0000;AF1=0.5;AC1=1;DP4=3777,0,3625,0;MQ=59;FQ=115;PV4=1,1,1,1 GT:PL:GQ 0/1:169,0,142:99 chr2:102968307+102968424 50 . C T 55 . DP=7588;VDB=0.0000;AF1=1;AC1=2;DP4=1528,0,2680,0;MQ=40;FQ=-63;PV4=1,1,1,1 GT:PL:GQ 1/1:88,36,0:69 chr2:102968307+102968424 56 . T C 57 . DP=7136;VDB=0.0000;AF1=0.5;AC1=1;DP4=2220,0,1620,0;MQ=41;FQ=29;PV4=1,1,1,0.14 GT:PL:GQ 0/1:87,0,56:59 I understand the positive numbers after FQ: The higher the better likelihood the variant calling is correct. But what do the negative numbers mean? Is -282 better than -10 or the opposite in regards to the SNP being heterozygous. Please help, Ben Pingilley |
From: Pingilley, B. J. <ben...@my...> - 2012-05-11 21:32:07
|
I am having trouble understanding the meaning of the FQ numbers. chr2:102968160+102968269 52 . C A 92 . DP=8801;VDB=0.0000;AF1=0.5005;AC1=1;DP4=1828,0,4996,0;MQ=59;FQ=3.02;PV4=1,1,0.00027,1 GT:PL:GQ 0/1:122,0,27:30 chr2:102968160+102968269 53 . A G 139 . DP=8799;VDB=0.0000;AF1=0.5;AC1=1;DP4=3777,0,3625,0;MQ=59;FQ=115;PV4=1,1,1,1 GT:PL:GQ 0/1:169,0,142:99 chr2:102968307+102968424 50 . C T 55 . DP=7588;VDB=0.0000;AF1=1;AC1=2;DP4=1528,0,2680,0;MQ=40;FQ=-63;PV4=1,1,1,1 GT:PL:GQ 1/1:88,36,0:69 chr2:102968307+102968424 56 . T C 57 . DP=7136;VDB=0.0000;AF1=0.5;AC1=1;DP4=2220,0,1620,0;MQ=41;FQ=29;PV4=1,1,1,0.14 GT:PL:GQ 0/1:87,0,56:59 I understand the positive numbers after FQ: The higher the better likelihood the variant calling is correct. But what do the negative numbers mean? Is -282 better than -10 or the opposite in regards to the SNP being heterozygous. Please help, Ben Pingilley |
From: Heng Li <lh...@sa...> - 2012-05-11 21:42:16
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FQ>0: a heterozygote; the call is more confident if |FQ|=FQ is larger FQ<0: a homozygote; the call is more confident if |FQ|=-FQ is larger Heng On May 11, 2012, at 5:31 PM, Pingilley, Benjamin J. wrote: > > I am having trouble understanding the meaning of the FQ numbers. > > chr2:102968160+102968269 52 . C A 92 . DP=8801;VDB=0.0000;AF1=0.5005;AC1=1;DP4=1828,0,4996,0;MQ=59;FQ=3.02;PV4=1,1,0.00027,1 GT:PL:GQ 0/1:122,0,27:30 > chr2:102968160+102968269 53 . A G 139 . DP=8799;VDB=0.0000;AF1=0.5;AC1=1;DP4=3777,0,3625,0;MQ=59;FQ=115;PV4=1,1,1,1 GT:PL:GQ 0/1:169,0,142:99 > chr2:102968307+102968424 50 . C T 55 . DP=7588;VDB=0.0000;AF1=1;AC1=2;DP4=1528,0,2680,0;MQ=40;FQ=-63;PV4=1,1,1,1 GT:PL:GQ 1/1:88,36,0:69 > chr2:102968307+102968424 56 . T C 57 . DP=7136;VDB=0.0000;AF1=0.5;AC1=1;DP4=2220,0,1620,0;MQ=41;FQ=29;PV4=1,1,1,0.14 GT:PL:GQ 0/1:87,0,56:59 > > I understand the positive numbers after FQ: The higher the better likelihood the variant calling is correct. But what do the negative numbers mean? Is -282 better than -10 or the opposite in regards to the SNP being heterozygous. > > Please help, > Ben Pingilley > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help -- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE. |
From: Tommaso M. <t....@cs...> - 2012-05-25 10:49:14
|
-- Tommaso Mazza, Ph.D. Bioinformatics unit Casa Sollievo della Sofferenza - Mendel Viale Regina Margherita 261 00198 Roma IT Tel: +39 06 44160526 Fax: +39 06 44160538 E-mail: t....@cs... Web page: http://www.css-mendel.it/ Personal web: http://www.tommasomazza.eu |
From: Eric L. <lyz...@gm...> - 2012-07-09 15:35:08
|
*Can anyone tell me how to calculate strand bias P-value in samtools?* |
From: Hansen, N. (NIH/N. [E] <nh...@ma...> - 2012-07-09 18:56:49
|
Hi Eric, It looks to me like a two-tailed Fishers exact test is being done on the counts for reference and non-reference bases on the forward and reverse strand, and the p-value is being reported on a phred scale, I.e., Q = 10*log_10(p). So we are testing the null hypothesis that the two alleles are distributed between the two strands in equal proportions. Hope that helps, --Nancy -- ************************************* Nancy F. Hansen, PhD nh...@nh... Comparative Genomics Unit, NHGRI 5625 Fishers Lane Rockville, MD 20852 Phone: (301) 435-1560 Fax: (301) 435-6170 From: Eric Liu <lyz...@gm...<mailto:lyz...@gm...>> Date: Mon, 9 Jul 2012 11:34:56 -0400 To: "sam...@li...<mailto:sam...@li...>" <sam...@li...<mailto:sam...@li...>> Subject: [Samtools-help] (no subject) Can anyone tell me how to calculate strand bias P-value in samtools? |
From: WATSON M. <mic...@ro...> - 2012-07-19 10:49:39
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Mick Watson Director of ARK-Genomics The Roslin Institute, R(D)SVS, University of Edinburgh Division of Genetics and Genomics Easter Bush Midlothian EH25 9RG United Kingdom Telephone number + 44 (0) 131 651 9208 Fax number +44 (0) 131 651 9105 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. |
From: Lana G. <lga...@gm...> - 2013-01-24 13:10:36
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http://healthylivinghabit.org/wp-admin/yahool321.php |
From: Erik A. <er...@q3...> - 2013-05-06 14:32:01
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samtools-1.1.19 This version always outputs this error if the input is a stream (since it's not seekable, I guess) [bam_header_read] EOF marker is absent. The input is probably truncated. We regularly wrap samtools so that it does the following: - always exits nonzero when input is corrupt (EOF marker absent, etc.), regardless of whether it worked - always exits nonzero when output/write fails |