I need to call SNPs from pooled RNA-seq data. In each pool, I have 2 or 3 individuals. I am following the GATK pipeline for this purpose.
What I wonder about, and this could be due to my lack of understanding of the SNP calling process from pooled data, if for a given position, one sees two alleles, how could one say whether this position is a heterozygote in one of the individuals or whether these two different alleles come from two homozygote individuals?
I would appreciate some comments on this. Thanks.