I'm trying to execute gatk somatic cnv workflow using human exome data. And I made PON and intervals files from normal bams or reference fasta file that used at this analysis. When I checked cnv_somatic_pair_workflow.input.json, I found two interval_list file should be set: "CNVSomaticPairWorkflow.intervals" and "CNVSomaticPairWorkflow.common_sites". What's the difference among the two interval_list files?
I found a description about the two files (https://app.terra.bio/#workspaces/help-gatk/Somatic-CNVs-GATK4).
|Picard- or GATK-style interval list of common sites to use for collecting allelic counts.|
CNVSomaticPairWorkflow.intervals: Picard or GATK-style interval list. For WGS, this should typically only include the autosomal chromosomes.
Based on the above, CNVSomaticPairWorkflow.intervals means interval_files with only autosome? So, should I set interval_files with only autosome as an argument of "CNVSomaticPairWorkflow.intervals"?
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