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Genotypes in vcf with a GQ=0
I'm using GATK version 3.7 and I have a problem similar to the point raised in 2015 and titled "Unexpected genotype likelihoods & genotype qualities".
I've used HaplotypeCaller to generate individual GVCFs and after that, have used GenotypeGVCFs on multiple individual samples.
In the resulting vcf, I have some genotypes 0/0 with a GQ=0, whereas I was waiting for genotypes ./. (I suppose that when 2 genotypes have the same probability, the genotype should be unknown).
Could you please tell me how to do to force GATK to put ./. when GQ=0 ?
I've tried the GenotypeGVCFs command with teh version 3.8 and there's the same problem.
Thank very much.