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I have generated a multi sample vcf file with haplotype caller followed by CombineGVFs -> VariantReCalibrator -> Apply Recalibration.
Now I would like to filter my variants (only SNPs) based on GQ, DP and allele depth ->
AD for homozygous alt calls,
for homozygous ref calls and
for heterozygous calls.
I know how to filter based on GQ/DP but for allele depth, is there a way of doing this? I'm not able to find a filter expression on allele depth, obviously, I am missing on something!