Need some help to understand VCF files (yes, I've read the info from 1kgenome and have some "basic" understanding of them).
In the genotype result, for example, I have the following SNP identified.
chr1 860461 G A 98 PASS GT:CQ:DP 1/1:98:4 ./.:98:5 ./.:98:5 0/0:.:.
The genotype for the 4 individuals are
AA, ?, ?, GG
My questions are
- why with read depth (DP) = 4 for individual #1, the genotype is "readable" and considered AA, whereas for individual #2, the read depth is 5, but the genotype cannot be called and hence ./.
- why for individual #4, nothing is readable but still there is this predicted GG genotype given.
- how did this SNP end up being given a "PASS" by the filter? To me, all 4 individuals have poor read at this position.
Any help? Great many thanks