Hello everyone! There is the following problem in my vcf file produced by GATK: a large proportion of heterozygous sites has a bias in allele depth values (AD). For example, AD is 43,7 which means that the 43 reads support one allele while 7 support another. In order to avoid possible false calls in GWAS, I want to switch such SNPs to no-calls (./.).
I know that it is possible to write a heavy-duty R or Python script substituting the heterozygous calls (0/1) for no-calls (./.) in case of significant AD bias, let's say when minor allele to major allele ratio is greater than 0.3. However, I wonder if there are ready-to-go solutions. I tried to find such a filter in GATK but failed.
In case if you faced a similar problem or know about the ready solution please share!
