pegasus_vcfMerger.sh launches the VCF merger pbs script. Inside that script, GATK VariantAnnotator is run on the merged VCF files, and it can optionally take some annotations like EXAC, COSMIC, 1kG, etc.. There is a conditional that skips these annotations if the recipe is 'cerberus' on line 241:
if [ "${RECIPE}" == "cerberus" ] ; then
If each recipe has a species attribute, then we can change this part to only run with human comparisons if the recipe is human.
pegasus_vcfMerger.shlaunches the VCF merger pbs script. Inside that script, GATK VariantAnnotator is run on the merged VCF files, and it can optionally take some annotations like EXAC, COSMIC, 1kG, etc.. There is a conditional that skips these annotations if the recipe is 'cerberus' on line 241:If each recipe has a species attribute, then we can change this part to only run with human comparisons if the recipe is human.