If two paired reads are overlapping, it means that the same molecule was sequenced twice. This is not desired, we want to do variant calling from a random collection of reads. Therefore we include only one of the bases in the pileup, unless -x option is given.
Well spotted, Colin. Petr On Tue, 2017-02-21 at 01:29 -0600, Jiri Nehyba wrote: > Hi Colin, > > you solved it! That is exactly what is needed. Thank you. Now I can > go to sleep and have sweet dreams. > > What is this overlap detection supposed to achieve? It seems to sets > reverse bases to 0 and perhaps takes their quality values and sums > them together with quality of forward bases. That would explain why G > values (38) most common in fastq/bam qualities are turn to m > (76=38+38) in mpileup. But what is purpose of that? > > Thank you, Colin. > > Jiri > > On 2/20/2017 11:18 PM, Colin Hercus wrote: > > Hi Jiri, > > > > That looks okay to me. > > > > Samtools does have an option > > > > -x, --ignore-overlaps disable read-pair overlap detection > > > > perhaps you need to set that. > > > > > > Colin > > > > On 21 February 2017 at 12:32, Jiri Nehyba <ji...@utexas.edu> wrote: > > > Hi Colin, > > > > > > here are couple of alignments from sam file. I used name sorting > > > for this demonstration to show reads of both orientations > > > together. Otherwise for mpile I am using the same bam file sorted > > > by plain sort command. > > > > > > Jiri > > > > > > M03964:25:000000000-AKT18:1:1101:1792:12037 83 chr16 > > > 3249344 42 173M = 3249342 -175 > > > ACAACCCAGAGTTGTTGGGAAAATGAAGTAAGGCCCAGTGTGTCCAAGTGCCTGGCAGAGAAGAG > > > CCCACAGGCAGGGAGTGCCTACCTTGTGTTCCAGGGCGACCTCCTCAATGGGGCGCACCCGGTGG > > > CCTTGGTGCTCCTGACTCAGACTGCAGATGAGGCAGATGGGCT > > > GGGFGGGGFGGGGGGGGGFGGGGGGGFGFFGGFGGFCDGGFGGGGGGGGGGGGGGGFGGGGGGGG > > > GGFFGGGFFGGCGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG > > > GGGGGGGGGGGGGGEGFGGGGGGGGGGGGGGGGEGGGGGFGGG AS:i:0 XN:i:0 > > > XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:173 YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1792:12037 163 chr16 > > > 3249342 42 173M = 3249344 175 > > > CAACAACCCAGAGTTGTTGGGAAAATGAAGTAAGGCCCAGTGTGTCCAAGTGCCTGGCAGAGAAG > > > AGCCCACAGGCAGGGAGTGCCTACCTTGTGTTCCAGGGCGACCTCCTCAATGGGGCGCACCCGGT > > > GGCCTTGGTGCTCCTGACTCAGACTGCAGATGAGGCAGATGGG GGGGGGGGGDGGGGGGGGG > > > CDGGF?FFFGAFGGGGGGGGFGGGGGGGGGGGGGGGGGGGEGGGGGGGGGFFECFF@EG7FCGGG > > > GFGGGDFFGFFGGGGGG?CCCEFE>FGGGFFFCD8CEECGGGGGGGGGGGGGGGFCFCCGGFGF> > > > F6F>FGGFGFDFFFAD>CAFFDAF AS:i:0 XN:i:0 XM:i:0 XO:i:0 > > > XG:i:0 NM:i:0 MD:Z:173 YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1856:12139 83 chr16 > > > 3248843 42 198M = 3248841 -200 > > > ACCCCTGCTCACTCTTCCCACCTTCCTCCCAGGGACGGATGGGCCATCAGCCACCTCTGACCTTA > > > CCAGAAAGCTCACTGCCTTCTCCTCCCCATAGGATCGCTGCTCCTCCCCTGATTTTCTCAGCTTC > > > TTCAGATGCTCCAGCTGCTTCTGAATTTTCTTCTGGAAAAACAGCACTTGTTGAAAAGCTTGAAT > > > TTG FDAFFFFGGGFGGDF@5C77GGC>GEGEGGFEEGGGGGGGGFGGGGFDEF6E8FGGGGFG > > > GGGGFFGGGEA9GGGGFGGGGGGGGGGGGGGDGGFGGGFGGGGGGGEGGGGGFGGGFGGGGGGGG > > > GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG > > > GGFGGGGG AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 > > > MD:Z:198 YS:i:-3 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1856:12139 163 chr16 > > > 3248841 42 198M = 3248843 200 > > > GGACCCCTGCTCACTCTTCCCACCTTCCTCCCAGGGACGGATGGGCCATCAGCCACCTCTGACCT > > > TACCAGAAAGCTCACTGCCTTCTCCTCCCCATAGGATCGCTGCTCCTCCCCTGATTTTCTCAGCT > > > TCTTCAGATGCTCCAGCTGCTTCTGACTTTTCTTCTGGAAAAACAGCACTTGTTGAAAAGCTTGA > > > ATT > > > GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGGGGG > > > GGGGGDEGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFGGGGGGGGGFGGGGGGFGGGG > > > EGGGCFGGGGGGGGGGGGFGGGGDGG+<D7FFGGFGFFFGFGFGF?5?FFFCFFF<@C5==@5@= > > > CFF AS:i:-3 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 > > > MD:Z:156A41 YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1936:12864 83 chr16 > > > 3254291 42 159M = 3254289 -161 > > > AATTTCTGGATTTGCGGGCGCCTTCTCCCCTGTAGAAATGGTGACCTCAAGGCTTCTAGGTCGCA > > > TCTTTCCCGAGGGCAGGTACACTTCGAAGGGCCTGCACTCCTTCTGCCCCGGGGCGCCCCCCGCC > > > AGCCCCTGCAGCCTCCCCGCGGAGCTGGC ?CGC:<FF<7:E>GGC>>DF88ECEGGEC<<+7@F > > > <CC?CFGGGDFGGGGGGGF9DGEE>E:C7FGGFEGGDEE<EGFGGFGGGGGEFFGE6G?;5@CGG > > > GGGGGGGGCEEE:GGGGGCCGGGGGCGGEDGF@7FGGGEGDGGGGGEEGCEE<GGGGDF > > > AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:159 > > > YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1936:12864 163 chr16 > > > 3254289 42 159M = 3254291 161 > > > AGAATTTCTGGATTTGCGGGCGCCTTCTCCCCTGTAGAAATGGTGACCTCAAGGCTTCTAGGTCG > > > CATCTTTCCCGAGGGCAGGTACACTTCGAAGGGCCTGCACTCCTTCTGCCCCGGGGCGCCCCCCG > > > CCAGCCCCTGCAGCCTCCCCGCGGAGCTG > > > FCFGAEFCF9CEGGFFFGGGGEEGG:<@<:@B<FGGGGGGAF,C<EGFGD@FCA@FFFFGC,9C: > > > @C@:FFG,EFGGGCB@F?@EFGFGCFDEG,BCGGGCEDCF>DFG9E9@DDFGC=6+@EEGG:@:E > > > GGG*=:8**?F4D=<49EE7DDG557C46 AS:i:0 XN:i:0 XM:i:0 XO:i:0 > > > XG:i:0 NM:i:0 MD:Z:159 YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1992:12226 83 chr16 > > > 3243623 42 218M = 3243621 -220 > > > GTCTAACACTCTTCAGATCATCAGAGAAGATGAGGTTGGGGTAAGCGGTTTCTGCATCCAGAATC > > > ACATTAACTGCAAAGAAAATTTGAATACCTAGGTAGGGGTCCATGGGCAACATCCCTACAGGGTT > > > CTCCCCACCTGCAGGAAACAGGGACAGGGTAGTTCTTCTGGAACGTGGTAGGGGAGAGCACAGGG > > > ATCCAGCAGGCCAGGGCCACTTG AFFFAFB:;+AFFA6FFFGFFGFGFFFGGGFFC>GG > > > D?C6FEGGGED@CFGGGFDCFDECE,38FFEAGGGFGGGGGGGGGGECGGGGGCEFF@F9A=GGE > > > CFGGGGGDGEFGGGGGGGGGGGGE@CGGGGGGGGGGGGGGGGGGFGGGGFFGGGFGGFGGFGGGG > > > GFGGFCGGGGGGGGDGGFCGFGGGFCFE@EFFDGFGFDCGGFF?GFFFFGFF AS:i:0 > > > XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:218 YS:i:-8 > > > YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:1992:12226 163 chr16 > > > 3243621 42 218M = 3243623 220 > > > AAGTCTAACACTCTTCAGATCATCAGAGAAGATGAGGTTGGGGTAAGCGGTTTCTGCATCCAGAA > > > TCACATTAACTGCAAAGAAAATTTGAATACCGAGGTAGGGGTCCATGGGCAACATCCCTACAGGG > > > TTATCCCCACCTGCAGGAAACAGGGACAGGGTAGTTCTTCTGGAACGTGGTAGGGGAGAGGACAG > > > GGATCCAGCAGGCCAGGGCCACT EEGCFDGFFEFFFD9CDEEFGGGFGGFGE,@@<AEF > > > ?C@E@FCFDGFFFE,@:EEFGFAE,B@FF,?AAFA9FFEFG,EFEFFF,,AFC,A<EFG,,@>CC > > > 4C@BC=?F?9EDCGGGF=,@DFGGGEC88D,+6@=2@D>E6=EFGGCG61=DDD?=*=?8*8=?F > > > 7CA+3<8@?5<F?>5@A5?)*:8))0::@BAD94>0*7((/58(/885>?04 AS:i:-8 > > > XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:96T35C57C27 > > > YS:i:0 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:2092:11235 99 chr16 > > > 3254128 42 189M = 3254130 191 > > > CGATATAAAGTAGGAAAGAACACAATTTACCGGTGACCGAATTTTCTGGATTTCCAGGGCCTTCC > > > TTCAGGTCCGCAGATGCCCCTCCATCCGGCGTGGGCCTTGCCCGGGGTTCTGTTGCCGAGTCCAG > > > ATTCGCAGCTGTCTTTTCTTCTAGAGTCAGGAGAGTTTCTGGATTTGCGGGCGCCTTCT > > > @+F@:FF@EFFG9F9FE<88FEF8,;C6CFG@E:FGGFG@@C,6CFGFFFF9FFGGGDGGGGFFD > > > FDF9FE,9EEE7++:,5,BFFGDG<EFGE+FEGG+:AFCF@,==FEF+8A,<FEG,?F7F@,3,8 > > > 733EEG@+>EGFFCCFEC;,@7BDC,3@9C8<*,*45,2,2,2,,29:19?CDD5::2; > > > AS:i:-12 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 > > > MD:Z:42G51A53C15A24 YS:i:-19 YT:Z:CP > > > M03964:25:000000000-AKT18:1:1101:2092:11235 147 chr16 > > > 3254130 42 189M = 3254128 -191 > > > ATATAAAGGAGGAAAGAACTCAATTTACCGGTGACCGAATGTTCTGGAGTTCCAGGGCCTTCCTT > > > CAGGTCCGCAGAGGCCCCTCCATCCGGAGTGGGCCTTGCCCGGGGTTCTGTTGCCGAGGCCAGAT > > > TCGCAGCTGTCTTTTCCTCTAGAGTCAGGAGAATTTCTGGATTTGCGGGCGCCTGCTCC > > > ))5A5655:8+8;1+1+4*+>:=+:81D8*C8@/?7GC9A70CFD;2**CFCC75;,@,EFE9C@ > > > 53++++8D8>D8+ECB83,+@EGFGGGCF?@44+++F=+C:@+<GF8F=,+7CDFEAA,GEFC@+ > > > 8:F8FC8FGFF8F@GCDC,9GFFF<<E<C,FFEDF6,GGGF6:::F7F7@@6CF7F@@, > > > AS:i:-19 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 > > > MD:Z:8T10A28T28T45T60T4 YS:i:-12 YT:Z:CP > > > > > > > > > > > > On 2/20/2017 9:01 PM, Colin Hercus wrote: > > > > Hi Jiri, > > > > > > > > Could you paste a few alignments from the SAM file. > > > > > > > > Colin > > > > > > > > On 21 February 2017 at 00:31, Jiri Nehyba <ji...@utexas.edu> > > > > wrote: > > > > > Hi Tom, > > > > > > > > > > Thanks for your help. > > > > > > > > > > I think Bowtie2 is not changing base qualities. To verify > > > > > that I > > > > > extracted from Bowtie2 bam file back the fastqs (bedtools > > > > > bamtofastq) > > > > > and looked base scores in FastQC - they look the same as > > > > > before > > > > > alignment. Bowtie2 is assigning alignment quality scores (bam > > > > > fifth > > > > > column) and those are mostly perfect (151364 from 158220 > > > > > bam/sam lines > > > > > have score 42). > > > > > > > > > > mpileup of samtools is changing the qualities. Below is one > > > > > line from > > > > > mpileup file (samtools mpileup -Q 0 -d 1000000 -f hg38.fa > > > > > PREFIX.bam > > > > > > PREFIX.pileup) . I folded long fifth and sixth column for > > > > > better > > > > > readibility. This is the position where the reads have C > > > > > instead of T > > > > > that is in reference. You might see about half of the bases > > > > > have > > > > > qualities higher than 0 (!), most frequent quality is m that > > > > > would > > > > > correspond to 109-33=76 on Illumina 1.8+ scale. Now original > > > > > qualities > > > > > both in fastqs and in bam/sam file don't have zeroes and the > > > > > most common > > > > > quality is G that is 38 on Illumina 1.8+ scale (lowest I can > > > > > see just by > > > > > looking at random places in bam file is + at the end of reads > > > > > that is > > > > > quality 10). > > > > > > > > > > > > > > > Jiri Nehyba > > > > > > > > > > chr16 3243407 T 928 > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC > > > > > CCCCCC.CCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC > > > > > CCCCCCCCCCCCCCCACCC > > > > > CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC.CCCCCCCCCCCC > > > > > CCCcccccccccccccccc > > > > > ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc > > > > > ccccccccccccccccccc > > > > > cccccccccccccccccccccccccccccccccccccccccccccccccccc,cccccccc > > > > > ccccccccccccccccccc > > > > > ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc > > > > > ccccccccccccccccccc > > > > > ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc > > > > > ccccccccccccccccccc > > > > > ccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc > > > > > acccccccccccccccccc > > > > > cccccccccccccccccccccccccccccccccccccccccccccccc > > > > > mhmmmmklgmlmmlmmmmmlmmmmmmmimlmmmljmml_mmmmm\llmmRkmmkjm_mmim > > > > > mmlmmkmmlmmkmmfllmm > > > > > m`mmlmmmmmmm[m_mmmbkkmimmmmemmmRmmmkiml`glmlmmmmhi`_mm]gmmmbm > > > > > kll]emLlkmmmmmkchgi > > > > > jmlmlkm_ilmmmmmmmmmikmXjmhjmm\jjjm`llmmimZmmh`mmmmmllRmjkmkmm > > > > > kmllmmmmmmmmmmmmm[m > > > > > l^mmmmlmmlmhmmmmmmmmmlmmmmlmmYmmiYmmmjmmmmkmmjImmmkmmmmmgmmmk > > > > > lmbimmlmkmmmmmlmmim > > > > > emmmmmlmmmlmmmmmmmmmmmmmmkimmmkhmmjlGlhmllmmmmllmm[mmmgmeimim > > > > > m_bmmkmQmamjmmlmmmf > > > > > mmhimmmmmlmmmmimmmml_mmjmmmmmlmmlmmmmimhemhR_^mm)mmjlmmmmkmmm > > > > > m`m!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!! > > > > > !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! > > > > > > > > > > > > > > > On 2/20/2017 6:38 AM, Thomas W. Blackwell wrote: > > > > > > > > > > > > I think this is a bowtie2 question, not a samtools > > > > > question. Why is > > > > > > bowtie2 setting those base call qualities to zero ? > > > > > > > > > > > > - tom blackwell - > > > > > > > > > > > > On Sun, 19 Feb 2017, Jiri Nehyba wrote: > > > > > > > > > > > >> Hi, > > > > > >> > > > > > >> I would like to ask for help with mutation calling using > > > > > >> samtools-bcftools. Specifically my problem is that I am > > > > > loosing > > > > > >> (almost) all my reverse bases and mutations are called > > > > > only on > > > > > >> forward bases (reads). > > > > > >> > > > > > >> I have installed last version of samtools and bcftools > > > > > (1.3.1). > > > > > >> > > > > > >> I have paired fastqs from amplicon panel libraries > > > > > sequenced on > > > > > >> Illumina MiSeq. I cut off the primer sequences using > > > > > Cutadapt, > > > > > >> aligned reads to hg38 genome with Bowtie2 (paired > > > > > alignment), sorted > > > > > >> and indexed bam file with samtools and then I used > > > > > following command: > > > > > >> > > > > > >> samtools mpileup -u -v -d 1000000 -f hg38.fa PREFIX.bam | > > > > > bcftools > > > > > >> call -c -v > > > > > >>> PREFIX.vcf > > > > > >> > > > > > >> Resulting vcf file looks like this (showing just three > > > > > rows and only > > > > > >> some of the fields) > > > > > >> > > > > > >> chr16 3243407 . T C 221.999 . DP=928; > > > > > . . . > > > > > >> ;DP4=1,0,462,0;MQ=42;FQ=-281.989;PV4=1,1,0.454462,1 GT:PL > > > > > >> 1/1:255,255,0 > > > > > >> chr16 3243888 . C T 221.999 . > > > > > DP=2982; . . . > > > > > >> ;DP4=2,0,1486,2;MQ=42;FQ=-281.989;PV4=1,0.458362,0.4298,1 > > > > > GT:PL > > > > > >> 1/1:255,255,0 > > > > > >> chr16 3243922 . A T 221.999 . > > > > > DP=2982; . . . > > > > > >> ;DP4=1,0,1486,4;MQ=42;FQ=- > > > > > 281.989;PV4=1,0.338485,0.450054,1 GT:PL > > > > > >> 1/1:255,255,0 > > > > > >> > > > > > >> What I don't like is the DP4 field that suggests extreme > > > > > strand bias. > > > > > >> > > > > > >> I tried to find out why are those reverse bases discarded > > > > > - there is > > > > > >> no reason for generally lower quality score - amplicons > > > > > are ligated > > > > > >> randomly in both orientations and I am getting both sides > > > > > of each > > > > > >> amplicon in R1 and R2 reads. > > > > > >> > > > > > >> The only thing that prevents the "loss" of the bases is > > > > > setting the Q > > > > > >> to 0, like that: > > > > > >> > > > > > >> samtools mpileup -u -v -Q 0 -d 1000000 -f hg38.fa > > > > > PREFIX.bam | > > > > > >> bcftools call -c -v > PREFIX.vcf > > > > > >> > > > > > >> Result: > > > > > >> > > > > > >> chr16 3243407 . T C 221.999 . DP=928; > > > > > . . . > > > > > >> ;DP4=2,1,462,463;MQ=42;FQ=-281.989;PV4=1,1,0.419714,1 > > > > > GT:PL > > > > > >> 1/1:255,255,0 > > > > > >> chr16 3243888 . C T 221.999 . > > > > > DP=2982; . . . > > > > > >> ;DP4=2,2,1489,1489;MQ=42;FQ=- > > > > > 281.989;PV4=1,0.493227,0.40081,1 GT:PL > > > > > >> 1/1:255,255,0 > > > > > >> chr16 3243922 . A T 221.999 . > > > > > DP=2982; . . . > > > > > >> ;DP4=4,3,1487,1488;MQ=42;FQ=-281.989;PV4=1,1,1,1 GT:PL > > > > > 1/1:255,255,0 > > > > > >> > > > > > >> If I set Q to more than 0, for example 1 I will again > > > > > loose almost > > > > > >> all reverse bases. > > > > > >> > > > > > >> Finally, a look at mpileup file obtained by this command: > > > > > samtools > > > > > >> mpileup -Q 0 -d 1000000 -f hg38.fa PREFIX.bam > > > > > > PREFIX.pileup > > > > > >> > > > > > >> I see that half of the bases is getting score ! that is 0 > > > > > : > > > > > >> > > > > > >> > > > > > >> > > > > > >> Thank you for your help, > > > > > >> > > > > > >> Jiri > > > > > >> > > > > > > > > > > > > > > > ----------------------------------------------------------- > > > > > ------------------- > > > > > Check out the vibrant tech community on one of the world's > > > > > most > > > > > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > > > > > _______________________________________________ > > > > > Samtools-help mailing list > > > > > Samtools-help@lists.sourceforge.net > > > > > https://lists.sourceforge.net/lists/listinfo/samtools-help > > > > > > > > > > > > > > > > > > > ------------------------------------------------------------------- > ----------- > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > Samtools-help mailing list > Samtools-help@lists.sourceforge.net > 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. ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, SlashDot.org! http://sdm.link/slashdot _______________________________________________ Samtools-help mailing list Samtools-help@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/samtools-help
