I am not from a population genetics background, but am doing a feasibility test using a few organisms for a bigger aim of determining allele specific expression (ASE). I am performing variant calling on DNA-seq samples from 4 water buffaloes (Bubalus bubalis) to determine heterozygous sites in each samples using GATK 188.8.131.52. I also have RNA-seq data of the 4 animals that will allow me to take my ASE project forward.
How important is hets value (heterozygosity)? I have read- https://gatkforums.broadinstitute.org/gatk/discussion/8603/heterozygosity. Is using the default human heterozygosity value of 0.001 is correct for my non-model organism?
I also came across this website: https://gatkforums.broadinstitute.org/gatk/discussion/8603/heterozygosity
How can I determine heterozygosity for my species? Where or What should I look into to know about this value for my non-model organism?
An easy explanation will be appreciated as this would help me to understand the weightage of this parameter.