vcf file from a pooled sample
I am having difficulty in understanding the vcf output of haplotype caller when I use it for a pool of two individuals. I set ploidy to 4 in this case.
When ploidy is 2, one get the heterozygote genotype as 0/1 which is understandable. In the case of ploidy equals to 4, how I can interpret such a genotype (GT:AD:DP:GQ:PL 0/0/0/1:8,3:11:5:95,0,5,24,232) given that this is a pooled sample so it is not possible to know the genotype. I just was wondering what this means.