Question: Understanding VCF file for downstream analysis
0
gravatar for upendrakumar.devisetty
22 months ago by
United States
upendrakumar.devisetty350 wrote:

I got this vcf file from my collaborator and I am so trying to understand this for the last few days but no avail. I needed to use this vcf for all downstream analysis such as Structure, PC, Linear Discriminant Analysis. I have worked with VCF files before but I never seen this kind before.

#CHROM  POS ID  REF ALT QUAL    FILTER  INFO    FORMAT  1KS 2861    2862    2A
Potrs007791 23342   .   G   T   427264.55   PASS    AC=342;AF=0.777;AN=440;BaseQRankSum=14.742;DP=16493;Dels=0.00;ExcessHet=32.5636;FS=1.803;HaplotypeScore=1.1332;InbreedingCoeff=-0.2081;MLEAC=342;MLEAF=0.777;MQ=34.94;MQ0=208;MQRankSum=-58.531;QD=26.19;ReadPosRankSum=4.181;SOR=0.995 GT:AD:DP:GQ:PL  B   B   B   B

Here 1KS, 2881, 2862 and 2A are samples and B here indicates Alternate SNP. Can someone help me convert this to regular VCF so that I can start using that? I understand that I need values for each of the GT:AD:DP:GQ:PL but I don't know how to get these from the INFO column.

snp gatk vcf • 968 views
ADD COMMENTlink written 22 months ago by upendrakumar.devisetty350
1

it looks like a VCF file but it's not (anymore) a VCF file.

ADD REPLYlink written 22 months ago by Pierre Lindenbaum118k

Is there a way to convert this to VCF file based on information in INFO column?

ADD REPLYlink written 22 months ago by upendrakumar.devisetty350

INFO column needs a header, and the header is missing. Nobody but your collaborator knows what are those "B" in the genotype columns.

ADD REPLYlink written 22 months ago by Pierre Lindenbaum118k

Ok. I will ask my collaborator. Thanks..

ADD REPLYlink written 22 months ago by upendrakumar.devisetty350
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