Using RNA-seq sequence to genotype known variants. I have used the following steps:
- GATK Haplotypecaller for variant calling
- Filtering possible RNA editing events.
- freebayes: Genotypes for the population at each position in the reference to get the homozygous reference.
- HWE cutoff 0.01
However, I found that most of the variants are failing the Hardy Weinberg Equilibrium test. Does any one have any suggestion for what might causes an excess of HWE failures?