Multisample vcf to table

Question

[Myggan]

Hi,

I've used freebayes for calling variants on a set of bamfiles with 1 sample in each bam file. I want to somehow get a good overview over the variants that also non-bioinformaticians can look at.

The VCF file looks something like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 CONTROL
chr1       46      .       ACACC   CCACA   8.58901e-15     .       AB=0;ABP=0;AC=0;AF=0;AN=5;AO=2;CIGAR=1X3M1X;DP=137;DPB=147;DPRA=0.314961;EPP=3.0103;EPPR=17.5948;GTI=0;LEN=5;MEANALT=1;MQM=33;MQMR=54.4254;NS=5;NUMALT=1;ODDS=78.0575;PAIRED=1;PAIREDR=0.977612;PAO=0;PQA=0;PQR=506;PRO=17;QA=14;QR=4464;RO=134;RPP=7.35324;RPPR=77.9423;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=83;SRP=19.6042;SRR=51;TYPE=complex;technology.ILLUMINA_HiSeq2500=1    GT:DP:RO:QR:AO:QA:GL    0:81:80:2614:0:0:0,-10  0:6:6:218:0:0:0,-10     0:10:8:262:2:14:0,-10   0:19:19:671:0:0:0,-10   0:21:21:699:0:0:0,-10
chr1       2146    .       G       A       9.16135e-15     .       AB=0;ABP=0;AC=0;AF=0;AN=5;AO=28;CIGAR=1X;DP=251;DPB=251;DPRA=0;EPP=5.80219;EPPR=11.1996;GTI=0;LEN=1;MEANALT=1;MQM=18.9643;MQMR=57.3318;NS=5;NUMALT=1;ODDS=92.9516;PAIRED=0.964286;PAIREDR=0.977578;PAO=0;PQA=0;PQR=0;PRO=0;QA=633;QR=8052;RO=223;RPP=63.8115;RPPR=5.82445;RUN=1;SAF=11;SAP=5.80219;SAR=17;SRF=99;SRP=9.09627;SRR=124;TYPE=snp;technology.ILLUMINA_HiSeq2500=1   GT:DP:RO:QR:AO:QA:GL    0:145:136:4920:9:154:0,-10      0:27:22:788:5:129:0,-10 0:16:13:471:3:75:0,-10  0:13:9:333:4:100:0,-10  0:50:43:1540:7:175:0,-10

I've tried using both gatk and snpsifts variantotable/extractfields tools, but it will only sum all the INFO counts and not keep them separated.

My goal is to get something like this:

CHR POS EFF.FIELD1 REF ALT QUAL SAMPLE1.RO SAMPLE1.AO SAMPLE2.RO SAMPLE2.AO SAMPLE3.RO SAMPLE3.AO SAMPLE4.RO SAMPLE4.AO CONTROL.RO CONTROL.AO
chr1 46 "geneX" ACACC CCACA 8.58901e-15 80 0 6 0 8 2 19 0 21 0

But the current options would give something like:

 CHR POS EFF.FIELD1 REF ALT QUAL RO AO
 chr1 46 "geneX" ACACC CCACA 8.58901e- 134 2

My feeling is that this should be fairly common, so just want to make sure I'm not reinventing the wheel here. Anyone have any idea?

Answer 1

[Lee Katz]

You should use the latest version of bcftools, and you should get exactly what you want. However you would have to take time to make the -f string perfect. For example:

bcftools query --print-header -f '%CHROM\t%POS\t%REF\t%ALT[\t%GT\t%RO\t%AO]\n' file.vcf.gz

[Myggan]

This worked very well! Thanks a lot!

[Myggan]

Thanks it sounds like it could do the trick! I'll try it today, thanks!

Answer 2

[kirannbishwa01]

Try vcf_simplify-v1.py https://github.com/everestial/vcf_simplify

Answer 3

[Ming Tommy Tang]

Have you seen this? https://www.broadinstitute.org/gatk/blog?id=7089

[Myggan]

I did try the VariantsToTable from gatk, but it won't keep my samples separated from what I can see as it sums upp the observations for each sample. Should it be able to do that?