The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
GenotypeGVCFs: How to bump up the number of alleles in the combined VCF record?
I'm on docker gatk 188.8.131.52, following gatk best practices (I think). But learning the tools.
I'm running GenotypeGVCFs on a genomicsDB input containing collated data from 2400 samples.
I'm getting a series of
Chromosome HanXRQChr01 position 1051626 (TileDB column 1051625) has too many alleles in the combined VCF record : 60 : current limit : 50. Fields, such as PL, with length equal to the number of genotypes will NOT be added for this location.
And I'd like to know if there's a way to bump up that limit. I don't see anything in the docs with a default of