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log10LikelihoodsOfAC are bad in GenotypeGVCFs 4.0.5.x when using -new-qual flag
I am trying to do joint genotyping on a large cohort of samples (~1000 WES samples)
First, I followed GATK best practices 4.0.4 as it was the latest version at that moment.
I encountered memory issues as reported earlier.
A solution to this was to use 4.0.5.x and add the '-new-qual' tag.
However, when doing so I encounter another error:
java.lang.IllegalArgumentException: log10LikelihoodsOfAC are bad 4.579892256552976E-21,NaN
I encounter this for all my regions.
So to summarize: I first do GenomicsDBImport with default options which returns true.
Next, GenotypeGVCFs starts, but after some milions of bases I encouter log10LikelihoodsOfAC error.
What could be the cause of this?