Bug with VariantFiltration with missing genotype info column?
I noticed that when I combine Gvcfs from multiple samples and genotype them, some samples that have missing genotypes are denoted by ./.:0,0:0.
1) It looks like VariantFiltration does not like it when it finds ./.:0,0:0. right after GT:AD:DP:GQ:PL column, i.e., when this happens for the first sample it has this problem, but if it happens for 2nd or nth sample, it seems okay..
2) Why are the missing genotypes denoted by ./.:0,0:0 and not ./.:0,0:0:0:0 , the GQ and PL fields dont have corresponding zeros. I am wondering if other tools that take vcf files, dont seem to like them due to this issue.
p.s I am using the latest build v3.4-46-gbc02625