-maxAltAlleles argument ignored in HC and genotypeGVCFs in GATK-3.7?
I have a similiar issue as described here:
I am using GATK version 3.7-0-gcfedb67 on poolseq data. I have 60 chromosomes per pool and calculated that the maximum genotype count should be 31470 when considering 3 alternate alleles.
The combination of -maxGT 31470 -maxNumPLValues 31470 -maxAltAlleles 3 works fine in HaplotypeCaller. However, running those output gvcfs in genotypeGVCFs with the same parameters I receive this error:
ERROR MESSAGE: the number of genotypes is too large for ploidy 60 and allele 9: approx. 7392009768
The programme considers 9 alleles although I have set -maxAltAlleles 3 explicitly, which should be 5 alleles including the reference and symbolic non-ref allele.
Any ideas why this is happening or tips how I can fix this?