Question: How to interpret vcf file (output of mkvcf) for complete genomics data
0
gravatar for MAPK
4.2 years ago by
MAPK1.5k
United States
MAPK1.5k wrote:

I have an output of mkvcf from cgatools where I have merged multigenome masterVar files. I would like to understand what  ./. , ./1 , 1/. ,  1|2 ,1|0 and 1/0 mean.

To give an example of my data: 

For the fields below 

GT:PS:FT:GQ:HQ:EHQ:GL:DP:AD:CGA_RDP 

I have all these outputs for different SNPs for one of the samples

SNP1  ./.:.:.:.:.,.:.,.:.:.:.,.:.

SNP2  0/0:.:.:.:.,.:.,.:.:.:.,.:.

SNP3  1|.:72697:VQLOW:.:30,.:30,.:-30,0,0:23:21,.:2

SNP4   0|.:72697:VQLOW:.:31,.:31,.:0,0,-31:.:.,.:.

SNP5 1/2:.:AMBIGUOUS:CTCTTT|-13&CTCTT|-17,CTCTTTT|-5&CTCT|-10&CTCTT|-11&CTCTTTTT|-16:42:42,42:42,42:-42,-42,-42,-42,0,-42:5:2,2:1

sequencing complete genomics • 1.1k views
ADD COMMENTlink modified 4.2 years ago by Pierre Lindenbaum127k • written 4.2 years ago by MAPK1.5k
2
gravatar for Pierre Lindenbaum
4.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

see the VCF spec: https://samtools.github.io/hts-specs/VCFv4.2.pdf

GT: Genotype, encoded as allele values separated by either of / or | . The allele values are 0 for the reference allele (what is in the REF eld), 1 for the rst allele listed in ALT, 2 for the second allele list in ALT and so on. ...
ADD COMMENTlink written 4.2 years ago by Pierre Lindenbaum127k
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