I have two individuals of the same animal (one male and one female water buffalo). I have RNAseq data from both the animals and I used mpileup and bcftools 'call' programs for variant calling. My aim is to find out allelic imbalance in a set of genes of interest.
Let me take an example of one variant in the resuted VCF file. For a particular variant ,one individual is heterozygous and the other is homozygous.
Since, allelic imbalance can only be found out through a heterozygous SNP, should I go ahead with the variants that are heterozygous in both the individuals? Or should I go ahead with the variants that are atleast heterozygous in at least one individual.
Thanks. PS- I am new to NGS and doing variant analysis for the first time