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Variant filtration by allelic balance bias
I'm trying to find a way to filter some heterozygous genotypes that might have been misassigned due to PCR or sequencing errors and result in a very unrealistic allelic balance bias like the following (bias greater than 1/3 or sometimes greater than 1/4):
I found that, in the past, GATK had the AlleleBalanceBySample annotation that would be very useful to remove the genotype assigned in such situations.
I know that I can do that using JEXL expressions sample by sample. However, when genotyping several samples together, iterating over the samples it's time consuming.
Do you know a faster way of doing such thing?
Thank you in advance.