Where do I find resources for using FilterVariantTranches with CNN_2D/CNN_1D scores?Answered
Documentation for FilterVariantTranches suggests using hapmap.vcf and mills.vcf resources to select cutoffs for CNN_2D and CNN_1D scores:
gatk FilterVariantTranches \ -V input.vcf.gz \ --resource hapmap.vcf \ --resource mills.vcf \ --info-key CNN_2D \ --snp-tranche 99.95 \ --indel-tranche 99.4 \ --invalidate-previous-filters \ -O filtered.vcf
I imagine these files need CNN_2D or CNN_1D scores. The "resources_broad_hg38_v0_Mills_and_1000G_gold_standard.indels.hg38" and "resources_broad_hg38_v0_hapmap_3.3" files are not scored for CNN_2D or CNN_1D so I assume they will not work.
Could you provide information on where to find these resources or other ways to run this tool?
Hi Rodrigo Cabrera,
The files don't need to be scored for CNN_1D or CNN_2D to be used as resources with FilterVariantTranches. They are just supposed to be known sites files.
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