confused about vcf representation for multiple samples
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xiaok...@gmail.com
Oct 29, 2014, 3:59:11 PM10/29/14
to delly...@googlegroups.com
Hi Tobias,
I tried to use delly to perform sv analysis for multiple samples together. command is like this: delly_v0.5.5_parallel_linux_x86_64bit -t DUP -o sv_INV.vcf -g /human/hg19.fa -q 30 tumor.bam normal1.bam normal2.bam ....
However, I am getting confused about the results represented using vcf (below is a sample excerpt) for multiple samples. I have several questions (forgive me if they seem to be stupid questions).
1. why the REF are all 'N' and QUAL are all '.' for all my vcf results.
2. how to interpret the samples columns. for example, how can I tell the inv event (for example, INV00038236N) happens in which sample?
3. how to use the format values of "GT:GL:GQ:FT:RC:DR:DV:RR:RV" to interpret sv event for each sample.
4. Do we have a detailed manual for delly?
Thank you very much.
-W
| #CHROM | POS | ID | REF | ALT | QUAL | FILTER | INFO | FORMAT | tumor | normal1 | normal2 | normal3 | normal4 | normal5 | normal6 | normal7 | normal8 |
| chr1 | 3326456 | INV00038236 | N | <INV> | . | PASS | CIEND=-369,369;CIPOS=-369,369;CHR2=chr1;END=230467789;PE=4;MAPQ=44;CT=5to5;IMPRECISE;SVLEN=227141333;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 1/1:-11.1982,-0.901323,0.0:9:LowQual:92999353:0:3:0:0 | 1/1:-4.39998,-0.301013,0.0:3:LowQual:94481145:0:1:0:0 | ./.:.,.,.:0:LowQual:94137321:0:0:0:0 | 1/1:-5.59862,-0.600682,0.0:6:LowQual:96112771:0:2:0:0 | 0/0:0.0,-1.09295,-24.8844:11:LowQual:47411589:10:1:0:0 | 0/0:0.0,-1.79645,-16.1903:18:PASS:46844335:6:0:0:0 | 0/0:0.0,-2.68925,-22.68:27:PASS:47292959:9:0:0:0 | 0/0:0.0,-3.28493,-26.6736:33:PASS:47292243:11:0:0:0 | |
| chr1 | 6099470 | INV00073918 | N | <INV> | . | LowQual | CIEND=-430,430;CIPOS=-430,430;CHR2=chr1;END=30028154;PE=2;MAPQ=36;CT=5to5;IMPRECISE;SVLEN=23928684;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 1/1:-5.19758,-0.599639,0.0:6:LowQual:10186700:0:2:0:0 | 1/1:-11.9978,-1.20194,0.0:12:LowQual:10903074:0:4:0:0 | 1/1:-6.3992,-0.601262,0.0:6:LowQual:10314769:0:2:0:0 | 1/1:-7.99689,-0.89998,0.0:9:LowQual:10694871:0:3:0:0 | 0/0:0.0,-8.72898,-123.099:87:PASS:5512227:29:0:0:0 | 0/0:0.0,-8.42803,-119.799:84:PASS:5209758:28:0:0:0 | 0/0:0.0,-9.3305,-126.999:93:PASS:5431453:31:0:0:0 | 0/0:0.0,-5.71888,-79.6993:57:PASS:5409010:19:0:0:0 | |
| chr1 | 8446627 | INV00026047 | N | <INV> | . | LowQual | CIEND=-378,378;CIPOS=-378,378;CHR2=chr1;END=78543590;PE=2;MAPQ=44;SR=83;SRQ=1.0;CONSENSUS=TCTTTTTCATGAAGGGCCTGTGTAAGTCTTTTGCTTATTTTTCAATGGATTGTCCTTTTCTTTTTCATTTGTAAGAGTTCGGGCCGGGCGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCCGAGGCGGGCGGATCACGAGGTCAGGAG;CT=5to5;PRECISE;SVLEN=70096963;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-23.283,0.0,-36.1828:233:PASS:32244281:0:0:10:7 | 0/1:-56.3806,0.0,-10.781:108:PASS:33437139:0:0:4:15 | 0/1:-32.0848,0.0,-20.285:203:PASS:32688986:0:0:6:9 | 0/1:-57.7745,0.0,-30.375:304:PASS:33528008:0:0:9:16 | 0/0:0.0,-12.6425,-184.199:126:PASS:16661735:36:0:42:0 | 0/1:-20.1551,0.0,-152.052:202:PASS:16221321:37:0:39:8 | 0/0:0.0,-9.33139,-136.399:93:PASS:16563798:31:0:31:0 | 0/1:-32.6605,0.0,-109.56:327:PASS:16530166:22:1:28:11 | |
| chr1 | 16022604 | INV00041912 | N | <INV> | . | LowQual | CIEND=-392,392;CIPOS=-392,392;CHR2=chr1;END=178948185;PE=2;MAPQ=34;SR=9;SRQ=0.927885;CONSENSUS=CCCAAAGTGCTGGGATTACAGGCGTGAGCCACCGCGCCCGGCCAAGCGATTTTCTTTGGTAGTATATTTTAATTCCTTGTTTTTTCAGTGTATCTATTACGGGTTTTT;CT=3to3;PRECISE;SVLEN=162925581;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-15.5922,0.0,-73.4763:156:PASS:63258726:20:0:24:8 | 0/1:-24.7764,0.0,-72.9699:248:PASS:64770122:20:0:22:9 | 0/0:0.0,-4.50439,-54.2889:45:PASS:64770898:28:0:15:0 | 0/1:-62.3687,0.0,-48.572:486:PASS:65883151:0:0:16:20 | 0/1:-7.15811,0.0,-179.644:72:PASS:32466838:49:0:49:6 | 0/1:-9.46092,0.0,-126.763:95:PASS:32086360:34:0:33:6 | 0/1:-2.36261,0.0,-138.761:24:PASS:32395787:23:0:37:4 | 0/0:0.0,-12.0363,-164.595:120:PASS:32396291:46:0:40:0 | |
| chr1 | 16801817 | INV00052896 | N | <INV> | . | PASS | CIEND=-301,301;CIPOS=-301,301;CHR2=chr1;END=17273996;PE=5;MAPQ=31;SR=4;SRQ=1.0;CONSENSUS=ATTATTAATCTGTATCATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTGAGACGGAGTCTTGCTCTGTTGCCCAGGCTGGAGTGCAGT;CT=3to3;PRECISE;SVLEN=472179;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-4.99624,0.0,-6.29657:50:PASS:97546:4:0:2:2 | 0/1:-2.49796,0.0,-3.79829:25:PASS:116989:1:0:1:1 | 0/0:0.0,-0.601698,-7.49964:6:LowQual:161498:0:0:2:0 | 0/1:-2.69796,0.0,-3.79816:27:PASS:111912:0:0:1:1 | 0/1:-21.4761,0.0,-67.0685:215:PASS:78300:14:0:24:9 | 0/1:-19.0791,0.0,-66.768:191:PASS:57664:15:0:25:9 | 0/1:-11.5858,0.0,-41.2866:116:PASS:54648:7:0:15:6 | 0/1:-25.9767,0.0,-55.6726:260:PASS:54681:11:0:21:11 | |
| chr1 | 16832462 | INV00053890 | N | <INV> | . | PASS | CIEND=-394,394;CIPOS=-394,394;CHR2=chr1;END=147995130;PE=5;MAPQ=38;CT=5to5;IMPRECISE;SVLEN=131162668;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 1/1:-6.49823,-0.600293,0.0:6:LowQual:49370721:0:2:0:0 | 1/1:-6.59924,-0.601302,0.0:6:LowQual:50368168:0:2:0:0 | 1/1:-16.1907,-1.79685,0.0:18:PASS:50413370:0:6:0:0 | 1/1:-8.09469,-0.897785,0.0:9:LowQual:51311536:0:3:0:0 | 0/0:0.0,-0.298281,-2.19725:3:LowQual:25271250:1:0:0:0 | 0/0:0.0,-0.298281,-2.19725:3:LowQual:24980080:1:0:0:0 | 0/1:-1.60241,0.0,-3.49829:16:PASS:25209113:2:1:0:0 | ./.:.,.,.:0:LowQual:25213953:0:0:0:0 | |
| chr1 | 22020908 | INV00043280 | N | <INV> | . | LowQual | CIEND=-378,378;CIPOS=-378,378;CHR2=chr1;END=78735810;PE=2;MAPQ=44;SR=3;SRQ=0.925;CONSENSUS=GATTACAGGCACATGCCACCACACCCAGCTAATTTTTGTATTTTTTGTAGAGACAGTGGTCTTGGTATGTTGTCCATGCTGGTCTCAAACTCCTGGCCAC;CT=5to5;PRECISE;SVLEN=56714902;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-11.9959,0.0,-3.19593:32:PASS:26632576:17:0:1:3 | 0/1:-7.89693,0.0,-3.49694:35:PASS:27374588:2:0:1:2 | ./.:.,.,.:0:LowQual:26945514:5:0:0:0 | 0/0:0.0,-0.602025,-8.79997:6:LowQual:27595359:5:0:2:0 | 0/1:-14.8939,0.0,-6.49401:65:PASS:13637830:30:0:2:4 | 0/1:-10.395,0.0,-6.09502:61:PASS:13373035:41:0:2:3 | 0/1:-5.3941,0.0,-14.194:54:PASS:13593949:23:0:4:2 | 0/1:-12.4939,0.0,-6.39672:64:PASS:13575650:25:0:2:4 | |
| chr1 | 27232146 | INV00030022 | N | <INV> | . | PASS | CIEND=-253,253;CIPOS=-253,253;CHR2=chr1;END=33516414;PE=35;MAPQ=39;SR=12;SRQ=1.0;CONSENSUS=AAGCCATCAAGATTCCTCTGTGAGGGATACCCTCCCTATACCAGGGCAAAAAATTACCCCTGATTACTTTCATTCTCATTGCACTGACCGGAACTTAGTTACAATGCCACGACTAGCAGCCGGGGT;CT=5to5;PRECISE;SVLEN=6284268;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 1/1:-47.1997,-3.31103,0.0:33:PASS:2716531:23:15:0:11 | 0/1:-41.0838,0.0,-14.8839:149:PASS:2891135:23:10:5:11 | 0/0:0.0,-0.902329,-11.0992:9:LowQual:2756135:31:0:3:0 | 0/1:-14.7949,0.0,-2.89504:29:PASS:2841712:29:10:1:4 | 0/1:-9.49291,0.0,-14.693:95:PASS:1489538:51:0:4:3 | 0/1:-9.59395,0.0,-10.394:96:PASS:1414630:50:0:3:3 | 0/1:-9.99302,0.0,-13.3929:100:PASS:1472556:45:0:4:3 | 0/1:-1.99402,0.0,-18.6939:20:PASS:1468666:38:0:5:1 | |
| chr1 | 28727947 | INV00049051 | N | <INV> | . | LowQual | CIEND=-364,364;CIPOS=-364,364;CHR2=chr1;END=81351537;PE=2;MAPQ=44;SR=45;SRQ=0.884615;CONSENSUS=AAGCTCCGCCTCCCGGGTTCACGCCATTCTCCTGCCTCAGCCTCCCAAGTAGCAATTTTCAAGTGAACTTTTAGACTCTCTTAAAGTTAGGATGGGATTATAGCTTTTTAAATGTATAAAGTAACTATTT;CT=3to3;PRECISE;SVLEN=52623590;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-24.2712,0.0,-81.8705:243:PASS:24972063:28:0:21:8 | 0/1:-19.6703,0.0,-89.3694:197:PASS:25470425:20:0:23:7 | 0/1:-28.9695,0.0,-83.3694:290:PASS:25234704:31:0:21:9 | 0/0:0.0,-6.62228,-96.7996:66:PASS:25814782:42:0:22:0 | 0/0:0.0,-11.7395,-171.599:117:PASS:12647128:47:0:39:0 | 0/1:-97.4409,0.0,-111.441:974:PASS:12482049:47:1:32:29 | 0/0:0.0,-10.2344,-149.599:102:PASS:12625372:41:0:34:0 | 0/1:-71.1509,0.0,-102.35:712:PASS:12611389:31:0:29:21 | |
| chr1 | 35007146 | INV00036939 | N | <INV> | . | PASS | CIEND=-333,333;CIPOS=-333,333;CHR2=chr1;END=218230521;PE=7;MAPQ=40;CT=5to5;IMPRECISE;SVLEN=183223375;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 1/1:-8.39994,-0.601999,0.0:6:LowQual:73400404:0:2:0:0 | ./.:.,.,.:0:LowQual:73798054:0:0:0:0 | ./.:.,.,.:0:LowQual:74429421:0:0:0:0 | 1/1:-3.99996,-0.300987,0.0:3:LowQual:75678394:0:1:0:0 | 0/0:0.0,-16.2534,-220.598:163:PASS:37140271:54:0:0:0 | 0/0:0.0,-13.243,-188.498:132:PASS:37005060:44:0:0:0 | 0/0:0.0,-0.728807,-103.899:7:LowQual:37126866:27:2:0:0 | 0/0:0.0,-11.7386,-159.298:117:PASS:37160600:39:0:0:0 | |
| chr1 | 46149176 | INV00079395 | N | <INV> | . | LowQual | CIEND=-392,392;CIPOS=-392,392;CHR2=chr1;END=189247039;PE=2;MAPQ=44;SR=41;SRQ=0.983974;CONSENSUS=ATCTCCTGACCTCGTGATCCGCCCGCCTCGGCCTCCCAAAGTGCTGAGATTACAGGCGTGAGCCACCGCGCCCGGCCTGAATATTTTTTATAACCTCTCTAAATCTTTTAAAAAATTAATTTCATTCAGTAACACATTAGTCCAGTAACAGAAGGA;CT=3to3;PRECISE;SVLEN=143097863;SVTYPE=INV;SVMETHOD=EMBL.DELLYv0.5.5;SOMATIC | GT:GL:GQ:FT:RC:DR:DV:RR:RV | 0/1:-6.99389,0.0,-15.7939:70:PASS:54623914:16:0:4:2 | 0/0:0.0,-0.602025,-8.79997:6:LowQual:55050544:11:0:2:0 | 0/1:-7.0949,0.0,-11.6949:71:PASS:55743916:11:0:3:2 | 0/1:-0.788952,0.0,-39.5887:8:LowQual:56601000:10:0:10:1 | 0/1:-32.7821,0.0,-43.1786:328:PASS:27661349:31:0:12:9 | 0/1:-15.1919,0.0,-14.7918:148:PASS:27624697:24:0:4:4 | 0/1:-28.8884,0.0,-11.8886:119:PASS:27675359:18:1:4:8 | 0/1:-69.7754,0.0,-14.4763:145:PASS:27705263:22:0:5:19 | |
xiaok...@gmail.com
Oct 29, 2014, 4:38:58 PM10/29/14
to delly...@googlegroups.com
Also, another related question is how you filter the somatic sv event using these samples information/columns?
Thank you.
-W
Tobias Rausch
Oct 30, 2014, 11:12:31 AM10/30/14
to xiaok...@gmail.com, delly...@googlegroups.com
There is now a python script to fix the REF allele:
python addRefAllele.py -v in.vcf -r <ref.fa> -o out.vcf
QUAL is optional and Delly doesn't set this value but this might change in future releases.
The sample columns contain the genotypes as described in the VCF-Spec (http://samtools.github.io/hts-specs/VCFv4.1.pdf).
Some further information on this is in the VCF header (and previous posts in this delly group).
There is no detailed Delly manual but there is a preliminary python script to filter somatic variants (python/somaticFilter.py).
-Tobias
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xiaok...@gmail.com
Oct 30, 2014, 12:11:13 PM10/30/14
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Tobias,
Thank you for your prompt answer.
But I am still confused how I can tell where the event, such as INV00038236N occur? I mean in which sample? Does it occur in at least one sample among all the samples tested? If so, what samples are they? I cannot find such information. I tried to figure out this from VCF headers but I cannot. Maybe I missed sth. The vcf header is as below. Could you clarify a bit on this? I am pretty new to this new version may be I got stupid for some points. Thank you very much.
But I am still confused how I can tell where the event, such as INV00038236N occur? I mean in which sample? Does it occur in at least one sample among all the samples tested? If so, what samples are they? I cannot find such information. I tried to figure out this from VCF headers but I cannot. Maybe I missed sth. The vcf header is as below. Could you clarify a bit on this? I am pretty new to this new version may be I got stupid for some points. Thank you very much.
| ##fileformat=VCFv4.1 | ||||||||||||||||
| ##fileDate=20141009 | ||||||||||||||||
| ##INFO=<ID=CIEND,Number=2,Type=Integer,Description="PE confidence interval around END"> | ||||||||||||||||
| ##INFO=<ID=CIPOS,Number=2,Type=Integer,Description="PE confidence interval around POS"> | ||||||||||||||||
| ##INFO=<ID=CHR2,Number=1,Type=String,Description="Chromosome for END coordinate in case of a translocation"> | ||||||||||||||||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the structural variant"> | ||||||||||||||||
| ##INFO=<ID=PE,Number=1,Type=Integer,Description="Paired-end support of the structural variant"> | ||||||||||||||||
| ##INFO=<ID=MAPQ,Number=1,Type=Integer,Description="Median mapping quality of paired-ends"> | ||||||||||||||||
| ##INFO=<ID=SR,Number=1,Type=Integer,Description="Split-read support"> | ||||||||||||||||
| ##INFO=<ID=SRQ,Number=1,Type=Float,Description="Split-read consensus alignment quality"> | ||||||||||||||||
| ##INFO=<ID=CONSENSUS,Number=1,Type=String,Description="Split-read consensus sequence"> | ||||||||||||||||
| ##INFO=<ID=CT,Number=1,Type=String,Description="Paired-end signature induced connection type"> | ||||||||||||||||
| ##INFO=<ID=IMPRECISE,Number=0,Type=Flag,Description="Imprecise structural variation"> | ||||||||||||||||
| ##INFO=<ID=PRECISE,Number=0,Type=Flag,Description="Precise structural variation"> | ||||||||||||||||
| ##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="Length of the SV"> | ||||||||||||||||
| ##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant"> | ||||||||||||||||
| ##INFO=<ID=SVMETHOD,Number=1,Type=String,Description="Type of approach used to detect SV"> | ||||||||||||||||
| ##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Somatic structural variant."> | ||||||||||||||||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||||||||||||||||
| ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Log10-scaled genotype likelihoods for RR,RA,AA genotypes"> | ||||||||||||||||
| ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | ||||||||||||||||
| ##FORMAT=<ID=FT,Number=1,Type=String,Description="Per-sample genotype filter"> | ||||||||||||||||
| ##FORMAT=<ID=RC,Number=1,Type=Integer,Description="Normalized high-quality read count for the SV"> | ||||||||||||||||
| ##FORMAT=<ID=DR,Number=1,Type=Integer,Description="# high-quality reference pairs"> | ||||||||||||||||
| ##FORMAT=<ID=DV,Number=1,Type=Integer,Description="# high-quality variant pairs"> | ||||||||||||||||
| ##FORMAT=<ID=RR,Number=1,Type=Integer,Description="# high-quality reference junction reads"> | ||||||||||||||||
| ##FORMAT=<ID=RV,Number=1,Type=Integer,Description="# high-quality variant junction reads"> | ||||||||||||||||
| ##FILTER=<ID=LowQual,Description="PE support below 3 or mapping quality below 20."> | ||||||||||||||||
| ##ALT=<ID=DEL,Description="Deletion"> | ||||||||||||||||
| ##ALT=<ID=DUP,Description="Duplication"> | ||||||||||||||||
| ##ALT=<ID=INV,Description="Inversion"> | ||||||||||||||||
| ##ALT=<ID=TRA,Description="Translocation"> | ||||||||||||||||
| ##ALT=<ID=INS,Description="Insertion"> | ||||||||||||||||
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