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CalculateGenotypePosteriors produces a bunch of zero coverage variants

Hi GATK Team,

we are running small targeted panels on GATK4. It seems, most of the Variants (~90%) are DP 0 Variants, emerging after applying CalculateGenotypePosteriors. Before this step we are running VQSR with over thirty exomes. Should we use external databases for CalculateGenotypePosteriors?

This is what we do now:

GATK version 4.0.4.0
${tool_gatk} --java-options "${javaArg_xms} ${javaArg_xmx}" CalculateGenotypePosteriors \ -R ${reference} \ -V ${outDirectory}/${variant_vcf}.vcf \ -O ${outDirectory}/${variant_vcf}.postCGP.vcf \ --supporting ${knownsite_hapmap} \ --pedigree ${pedigree}

Greetings
Martin

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