How to interpret vcf file (output of mkvcf) for complete genomics data

Question

[MAPK]

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

Answer 1

[Pierre Lindenbaum]

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. ...