Holiday Notice:
The Frontline Support team will be slow to respond December 17-18 due to an institute-wide retreat and offline December 22- January 1, while the institute is closed. Thank you for your patience during these next few weeks. Happy Holidays!

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



Sign In or Register to comment.