No variants with GenotypeGVCFs on polyploid samples

AmineAmine Member
edited February 1 in Ask the GATK team

Hello, I have two bam files with sequenced pooled individuals (16 and 20 individuals). I ran Haplotypecaller (gatk 3.8) by setting the ploidy option to 32 and 40 respectively for each of my samples. When I ran GenotypeGVCFs, I get an empty file with no variants. Does GenotypeGVCFs is not supporting these polyploidy levels?
As I’m interested only in the DP and AD counting, I'm thinking to try with ploidy 2, but I don’t know if this setting would change the AD and DP fields?

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