From: Peter C. <p.j...@go...> - 2013-05-06 14:43:57
|
On Mon, May 6, 2013 at 3:31 PM, Erik Aronesty <er...@q3...> wrote: > 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 This is worth reminding people about - I reported this regression 7 months ago: https://github.com/samtools/samtools/issues/18 Peter |
From: cristina z. <zib...@gm...> - 2013-05-02 20:09:23
|
Hi, * I'm using a SunOs Solaris 11 platform and I'm having issues compiling the samtools* am2bcf_indel.c: In function ‘bcf_call_gap_prep’: bam2bcf_indel.c:408:3: warning: implicit declaration of function ‘alloca’ bam2bcf_indel.c:408:10: warning: incompatible implicit declaration of built-in function ‘alloca’ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. errmod.c -o errmod.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sample.c -o sample.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. cut_target.c -o cut_target.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. phase.c -o phase.o phase.c: In function ‘phase’: phase.c:404:3: warning: array subscript has type ‘char’ phase.c:404:3: warning: array subscript has type ‘char’ phase.c:404:3: warning: array subscript has type ‘char’ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam2depth.c -o bam2depth.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. padding.c -o padding.o padding.c: In function ‘bam_pad2unpad’: padding.c:173:5: warning: format ‘%ld’ expects type ‘long int’, but argument 5 has type ‘size_t’ gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedcov.c -o bedcov.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bamshuf.c -o bamshuf.o gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview_curses.c -o bam_tview_curses.o bam_tview_curses.c:7:2: warning: #warning "_CURSES_LIB=1 but NCURSES_VERSION not defined; tview is NOT compiled" In file included from bam_tview.h:11:0, from bam_tview_curses.c:19: faidx.h:76:50: error: expected ‘;’, ‘,’ or ‘)’ before ‘register’ bam_tview_curses.c:287:2: warning: #warning "N*o curses library is available; tview with curses is disabled."* *** Error code 1 make: Fatal error: Command failed for target `bam_tview_curses.o' Current working directory /home/czibett1/samtools/samtools-0.1.19 *** Error code 1 The following command caused the error: target=`echo all-recur | sed s/-recur//`; \ wdir=`pwd`; \ list='. bcftools misc'; for subdir in $list; do \ cd $subdir; \ make CC="gcc" DFLAGS="-D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1" CFLAGS="-g -Wall -O2" \ INCLUDES="-I." LIBPATH="" $target || exit 1; \ cd $wdir; \ done; *make: Fatal error: Command failed for target `all-recur'* *I tried to make clean and modify the Makefile as follows* `-D_CURSES_LIB=1' to `-D_CURSES_LIB=0' at the line starting with `DFLAGS=', and comment out the line starting with `LIBCURSES='. as suggested in the INSTALL file *but I still get an error. *(this happens , I checked in the package manager and it seems zlib 1.2.3 is installed and I also installed the GNU ncurses 5.9)* * thanks |
From: Nadia B. <niu...@gm...> - 2013-08-05 09:36:04
|
Hi, i want to get a sorted file from samtools,my data files come from Bowtie in sam and std format but when i run samtools with sam file to get a bam or sorted file it generates an error ,could you help me? this error: [bam_header_read] EOF marker is absent. The input is probably truncated. [bam_header_read] invalid BAM binary header (this is not a BAM file). regards Nadia |
From: Peter C. <p.j...@go...> - 2013-08-05 10:29:15
|
On Mon, Aug 5, 2013 at 10:35 AM, Nadia Barjaste <niu...@gm...> wrote: > Hi, > > i want to get a sorted file from samtools,my data files come from Bowtie in > sam and std format but when i run samtools with sam file to get a bam or > sorted file it generates an error > ,could you help me? > this error: > [bam_header_read] EOF marker is absent. The input is probably truncated. > [bam_header_read] invalid BAM binary header (this is not a BAM file). > > regards > Nadia What was the command you typed? Did you give samtools a SAM file when it was expecting a BAM file? Peter |
From: Sendu B. <sb...@sa...> - 2013-08-05 10:39:18
|
On 5 Aug 2013, at 10:35, Nadia Barjaste <niu...@gm...> wrote: > Hi, > > i want to get a sorted file from samtools,my data files come from Bowtie in sam and std format but when i run samtools with sam file to get a bam or sorted file it generates an error > ,could you help me? > this error: > [bam_header_read] EOF marker is absent. The input is probably truncated. > [bam_header_read] invalid BAM binary header (this is not a BAM file). samtools always assume you are supplying it a bam file, which is perhaps counter-intuitive when you want to use it to convert a sam file to a bam file. $ samtools view -h shows you that you must supply -Sb, which tells samtools your input file is a sam file, and you want your output file to be a bam file. $ samtools view -Sb input.sam -o output.bam -- 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: Sendu B. <sb...@sa...> - 2013-08-05 15:08:55
|
(you should reply back to the list) The option in samtools view you need is -S, not -s. Again, read the help with -h. ./samtools view -b -S heg.sam > heg.bam On 5 Aug 2013, at 16:00, Nadia Barjaste <niu...@gm...> wrote: > > these are my commands: > at first i used Bowtie , "./bowtie-align -x chbt2 -U output.fastq -S heg.sam > after it i used samtools like this > ./samtools view -bs heg.sam > or > ./samtools view -b -s heg.sam>heg.bam > ./samtools sort -n heg.bam > all of the above samtools command returns error > > > On Mon, Aug 5, 2013 at 3:09 PM, Sendu Bala <sb...@sa...> wrote: > On 5 Aug 2013, at 10:35, Nadia Barjaste <niu...@gm...> wrote: > > Hi, > > > > i want to get a sorted file from samtools,my data files come from Bowtie in sam and std format but when i run samtools with sam file to get a bam or sorted file it generates an error > > ,could you help me? > > this error: > > [bam_header_read] EOF marker is absent. The input is probably truncated. > > [bam_header_read] invalid BAM binary header (this is not a BAM file). > > > samtools always assume you are supplying it a bam file, which is perhaps counter-intuitive when you want to use it to convert a sam file to a bam file. > > $ samtools view -h > shows you that you must supply -Sb, which tells samtools your input file is a sam file, and you want your output file to be a bam file. > > $ samtools view -Sb input.sam -o output.bam -- 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: Nadia B. <niu...@gm...> - 2013-08-05 15:39:56
|
Hi, i want to get a sorted file from samtools to process,this is a command i use "./samtools sort -o heg1.bam outstd" but i get this error "EOF marker is absent .The input is probably truncated invalid BAM binary header (this is not a BAM file) please help me in command using . Regars Nadia |
From: David S. <dav...@ma...> - 2013-08-06 15:20:10
|
Hi Nadia, This means that your BAM file is not complete. The "End Of File" marker is absent. To try see if you can view any reads by: $ samtools view heg1.bam | view If so, the BAM is just truncated, and try to re-acquire the BAM file from the source. If not, heg1.bam is probably not a BAM file. Regards, David ________________________________ From: Nadia Barjaste [niu...@gm...] Sent: August 5, 2013 11:39 AM To: sam...@li... Subject: [Samtools-help] (no subject) Hi, i want to get a sorted file from samtools to process,this is a command i use "./samtools sort -o heg1.bam outstd" but i get this error "EOF marker is absent .The input is probably truncated invalid BAM binary header (this is not a BAM file) please help me in command using . Regars Nadia |
From: Shohini G. <sgh...@jh...> - 2014-06-30 14:36:00
|
How do I add the directory containing the picard tools .jar files to my path? I am on Mac OS X. |
From: Alec W. <al...@br...> - 2014-06-30 20:42:30
|
Hi Shohini, It wouldn't do you any good to put these on your path, because the Picard jars are not directly executable on most OSs, including (at least for me) OS X. I.e. the program to be executed is 'java', not the Picard jar. -Alec On 6/30/14, 9:35 AM, Shohini Ghosh wrote: > > How do I add the directory containing the picard tools .jar files to > my path? I am on Mac OS X. > > > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > > > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help |
From: Marcel M. <mar...@tu...> - 2014-07-01 06:40:36
|
On 2014-06-30 22:42, Alec Wysoker wrote: > It wouldn't do you any good to put these on your path, because the > Picard jars are not directly executable on most OSs, including (at least > for me) OS X. I.e. the program to be executed is 'java', not the Picard > jar. Perhaps this is the right time for a suggestion for the Picard developers: Debian/Ubuntu provides with its picard-tools package a simple shell wrapper script that it installs as /usr/bin/picard-tools. You can then run picard like this: picard-tools FastqToSam I find this extremely convenient. Even when I'm not on Ubuntu, I often add such a wrapper script to my PATH. Would it be an idea to make this or something like it part of the official Picard distribution? Marcel |
From: Alec W. <al...@br...> - 2014-07-03 13:54:14
|
Hi Marcel, We tend to be reluctant to distribute something like this for the following reasons: * It increases support burden; * It's hard to create something that satisfies everyone's needs; * Since it doesn't require changes to the Java source, anyone can do this. If you have wrappers that you think would be useful for the community, perhaps you could distribute them somewhere (github?). I should also note that in the not-to-distant future the Picard command-line tools will be moving to the samtools model, i.e. a single executable to which you specify which program you want to run. I think in that case a single script will do, and you can easily create one that is appropriate for your needs. -Alec On 7/1/14, 2:40 AM, Marcel Martin wrote: > On 2014-06-30 22:42, Alec Wysoker wrote: >> It wouldn't do you any good to put these on your path, because the >> Picard jars are not directly executable on most OSs, including (at least >> for me) OS X. I.e. the program to be executed is 'java', not the Picard >> jar. > Perhaps this is the right time for a suggestion for the Picard > developers: Debian/Ubuntu provides with its picard-tools package a > simple shell wrapper script that it installs as /usr/bin/picard-tools. > You can then run picard like this: > > picard-tools FastqToSam > > I find this extremely convenient. Even when I'm not on Ubuntu, I often > add such a wrapper script to my PATH. Would it be an idea to make this > or something like it part of the official Picard distribution? > > Marcel > > > ------------------------------------------------------------------------------ > Open source business process management suite built on Java and Eclipse > Turn processes into business applications with Bonita BPM Community Edition > Quickly connect people, data, and systems into organized workflows > Winner of BOSSIE, CODIE, OW2 and Gartner awards > http://p.sf.net/sfu/Bonitasoft > _______________________________________________ > Samtools-help mailing list > Sam...@li... > https://lists.sourceforge.net/lists/listinfo/samtools-help |
From: Kevin <kev...@mh...> - 2014-12-04 20:10:25
|
remove this email from the list..I have another one I am having this sent to .so this is a duplicate |
From: John M. <jm...@sa...> - 2014-12-08 10:24:56
|
On 4 Dec 2014, at 17:52, Kevin <kev...@mh...> wrote: > remove this email from the list….I have another one I am having this sent to …so this is a duplicate Presuming you are asking for your @mho.com email address to be unsubscribed from the mailing list, I have done so. If you meant something else, please feel free to subscribe again. For those wishing to unsubscribe from the mailing list: every message from the list has a link at the bottom of it -- https://lists.sourceforge.net/lists/listinfo/samtools-help -- that includes a form for unsubscribing. John -- 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: Denis G. <s.a...@gm...> - 2015-05-01 13:01:19
|
Dear samtools team, For some further application i need change chromosome names in my bam files. samtools view example.bam | head -n2 FCC0U42ACXX:2:2103:13375:132773#ACTACAAG 99 SL2.40ch04 1 29 100M = 358 459 CATCACGGCCAATCCAACTCATTTTCAATGTCAAACGAGCCTCGAAGCGCGCATACCCCCCATTTCGACGATTTTTGTGTGCTATAGCAAAACACTTTTT @@CFDDFADHHDHIGBBHHG@HHHGGEHIIGGGIDH@@GGGCEFAECFGG<?<ABEECC?;233@A ?BB3)2??CA@BC<8CA>AD@@>C9?AA<:((:@ XT:A:U NM:i:3 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:86C4C2T5 RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part5.1.fq.bam FCC0U42ACXX:2:1306:12617:192543#ACTACAAG 89 SL2.40ch04 2 37 100M = 2 0 ATCACGGCCAATCCACCTCATTTTCAAGGTCAAACGAGCCTCGAAGCGCGCATACCCCCCATTTCGACGATTTTTGTGTGCTATACCAAACCATTTTTTG ?85&>>3B<:42213(3>@@CC>4(CCDCC<D?55BDDBDDDDDDDDDDDDC:5DJIIEIIIG@GGGJIFJJIJJIIJJIJIJIHIJHHDHHFFFFFCCB XT:A:U NM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:15A11T72 RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part4.1.fq.bam Then i applied the command: samtools view -H example.bam | sed -r 's/SL2.40ch//g' | samtools reheader - example.bam >test.bam 2>outErr.txt Then verify again with command: samtools view test.bam | head -n2 FCC0U42ACXX:2:2103:13375:132773#ACTACAAG 99 04 1 29 100M = 358 459 CATCACGGCCAATCCAACTCATTTTCAATGTCAAACGAGCCTCGAAGCGCGCATACCCCCCATTTCGACGATTTTTGTGTGCTATAGCAAAACACTTTTT @@CFDDFADHHDHIGBBHHG@HHHGGEHIIGGGIDH@@GGGCEFAECFGG<?<ABEECC?;233@A ?BB3)2??CA@BC<8CA>AD@@>C9?AA<:((:@ XT:A:U NM:i:3 SM:i:29 AM:i:29 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:86C4C2T5RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part5.1.fq.bam FCC0U42ACXX:2:1306:12617:192543#ACTACAAG 89 04 2 37 100M = 2 0 ATCACGGCCAATCCACCTCATTTTCAAGGTCAAACGAGCCTCGAAGCGCGCATACCCCCCATTTCGACGATTTTTGTGTGCTATACCAAACCATTTTTTG ?85&>>3B<:42213(3>@@CC>4(CCDCC<D?55BDDBDDDDDDDDDDDDC:5DJIIEIIIG@GGGJIFJJIJJIIJJIJIJIHIJHHDHHFFFFFCCB XT:A:U NM:i:2 SM:i:37 AM:i:0 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:15A11T72RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part4.1.fq.bam So it looks Ok. But then the command: samtools view -h test.bam | sed -rn '/SL2.40ch/p' >test.txt 2>outErr.txt find out a number of strings like this: FCC0U42ACXX:2:1104:6995:181777#ACTACAAG 83 04 623 29 59M1I40M = 234 -488 CTTGTGCTATAGCAAACCATTTTTTGGGTTATCCGGATTCCGACGTTAAAAATGCCATATTTTTTTGTGGACGTCTGTCAAGACCTTGGCTATGCATCCG ??94CCCEDDCCBBCCCC@CBBA?BBCC@2BBBCCCB@CEDAAECAIIIIIIIIGHGFGBGIGIGEIGHIGGGIHCGGCIIGFIIIIHHGHHFFFFFCCC XT:A:R NM:i:2 SM:i:0 AM:i:0 X0:i:2 X1:i:1 XM:i:1 XO:i:1 XG:i:1 MD:Z:29G69 XA:Z:SL2.40ch01,-74867066,100M,4;SL2.40ch04,-623,59M1I40M,2; RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part0.1.fq.bam FCC0U42ACXX:2:1305:8246:167295#ACTACAAG 83 04 679 60 100M = 309 -470 TATTTTTTTGTGGACGTCTGTCAAGACCTTGGCTATGCATCCGATTTTCCTTCATGGACATTCCAACCCATTTTCAAGGTCAAACGAGCCCCGAAGTGCG >BBB?A8DDDDDDBDDCDDCCDCC@ :DDDDDCCDECBDDDFFCFGHHEJIHEHEAGGAIHF@IGGBJJIGJJIEIJJIIHIGGGJJJHHHGHFFFFFCCC XT:A:U NM:i:3 SM:i:23 AM:i:23 X0:i:1 X1:i:1 XM:i:3 XO:i:0 XG:i:0 MD:Z:0A0T0A97 XA:Z:SL2.40ch04,-680,2M1I97M,1; RG:Z:120512_I238_FCC0U42ACXX_L2_SZAXPI008746-45_1.fq.gz.clean.dup.clean.gz.part4.1.fq.bam You can see the strings contain old chromosome name and further software (Conifer) also has found it and rise an error. My question what is wrong in my commands? How i can completely remove the old chromosome names from my bam files? Regards, Denis |
From: Mónica F. <mc...@gm...> - 2015-05-19 14:40:40
|
mc...@gm... |
From: Robert D. <rm...@sa...> - 2018-01-26 15:39:51
|
Samtools (and HTSlib) version 1.7 is now available from GitHub and SourceForge. https://sourceforge.net/projects/samtools/ https://github.com/samtools/htslib/releases/tag/1.7 https://github.com/samtools/samtools/releases/tag/1.7 BCFtools 1.7 will follow soon. The main changes are listed below: ---------------------------------------------------------------------------- htslib - changes v1.7 ---------------------------------------------------------------------------- * BAM: HTSlib now supports BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8). * BCF/VCF: - Removed the need for long double in pileup calculations. - Sped up the synced reader in some situations. - Bug fixing: removed memory leak in bcf_copy. * CRAM: - Added support for HTS_IDX_START in cram iterators. - Easier to build when lzma header files are absent. - Bug fixing: a region query with REQUIRED_FIELDS option to disable sequence retrieval now gives correct results. - Bug fixing: stop queries to regions starting after the last read on a chromosome from incorrectly reporting errors (#651, #653; reported by Imran Haque and @egafni via pysam). * Multi-region iterator: The new structure takes a list of regions and iterates over all, deduplicating reads in the process, and producing a full list of file offset intervals. This is usually much faster than repeatedly using the old single-region iterator on a series of regions. * Curl improvements: - Add Bearer token support via HTS_AUTH_LOCATION env (#600). - Use CURL_CA_BUNDLE environment variable to override the CA (#622; thanks to Garret Kelly & David Alexander). - Speed up (removal of excessive waiting) for both http(s) and ftp. - Avoid repeatedly reconnecting by removal of unnecessary seeks. - Bug fixing: double free when libcurl_open fails. * BGZF block caching, if enabled, now performs far better (#629; reported by Ram Yalamanchili). * Added an hFILE layer for in-memory I/O buffers (#590; thanks to Thomas Hickman). * Tidied up the drand48 support (intended for systems that do not provide this function). ---------------------------------------------------------------------------- samtools - changes v1.7 ---------------------------------------------------------------------------- * HTSlib, and so samtools, now support BAMs which include CIGARs with more than 65535 operations as per HTS-Specs 18th November (dab57f4 and 2f915a8). * samtools quickcheck will now write a warning to stderr if it finds any problems. These messages can be suppressed with a new `-q` option. * samtools markdup can now mark supplementary alignments of reads where the primary alignment is found to be a duplicate. Supplementary marking can be turned on by passing the `-S` option to markdup. When this option is enabled, all the alignment data will be written to a temporary file so that supplementary alignments that occur before a duplicated primary can be correctly marked in the final output. The location of this temporary file can be influenced using the new `-T` option. * samtools view now supports HTSlib's new multi-region iterator. This can be enabled by passing the `-M` option to view. When using this option: - The BED filter (`-L` option) will use the index to skip through the file - Reads from overlapping regions will only be output once * samtools bedcov will now ignore BED comment and header lines (#571; thanks to Daniel Baker). * samtools collate now updates the @HD SO: and GO: tags, and sort will remove a GO: tag if present. (#757; reported by Imran Haque). * Bug-fixes: - maq2sam now checks for input files that end early. (#751; patch supplied by Alexandre Rebert of the Mayhem team, via Andreas Tille from Debian.) - Fixed incorrect check when looking up header tags that could lead to a crash in samtools stats. (#208; thanks to Dave Larson.) - Fixed bug in samtools fastq `-O` option where it would fail if the OQ tag in the input file had an unexpected type. (#758; reported by Taejeong Bae) - The MD5 calculations in samtools dict and md5fa did not handle non-alphabetic characters in the same way as the CRAM MD5 function. They have now been updated to match. (#704; reported by Chris Norman). - Fix possible infinite loop in samtools targetcut. - Building bam_tview_curses should no longer fail if a curses header file cannot be found. Rob Davies rm...@sa... The Sanger Institute http://www.sanger.ac.uk/ Hinxton, Cambs., Tel. +44 (1223) 834244 CB10 1SA, U.K. Fax. +44 (1223) 494919 -- The Wellcome 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: Jody P. <jod...@gm...> - 2018-05-01 08:58:48
|
Hi All, I have very noisy reads and am trying to call SNPs/indels. I'm runinig into some trouble when truing to use the 'samtools mpileup | bcftools call' combination. It seems to incorrectly be calling very long indels where it looks like there is not support. For example: 'samtools mpileup -f ref.fa sample.bam -r Chromosome:198940-198940' produces: Chromosome 198940 C 37 .,.-1A.-1A...-1A.-1A.-1A.,-1a.-1A.,-1a,-1a.,.-1A,,.-1A,,+1a,+1a,.-1A,,-1a.,-1a,-1a,,-1a,-1a.-1A,-1a. 06?5/<:8>/4<?3691465<3354.08:23:11@3C This looks fine... however when I try to call the genotype with bcftools I get a very long indel. 'samtools mpileup -ugf ref.fa sample.bam -r Chromosome:198940-198940 -t AD | bcftools call -mv' produces: |