I am working with GATK 18.104.22.168 and am attempting to use the CollectAllelicCounts function as part of a somatic CNV Workflow. I need some additional help with the interval list that is to be used with the "-L" option. In Footnote #9 of the (How to part II) Sensitively detect copy ratio alterations and allelic segments tutorial, it makes reference to the SNPs-only gnomAD VCF files available in the GATK Resource Bundle but unfortunately that link is no longer valid. When I go to the Google Cloud Platform (https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0) I don't see the gnomAD SNPs-only VCF file as an option to download. Can you please help me with this? Is this file available for download somewhere? Or am supposed to create it myself as part of the workflow? I am working with WGS data from tumor and matched normal samples.
Please sign in to leave a comment.