What interval should I give to CollectAllelicCounts for somatic cnv in exome?

afzmafzm Member
edited December 2018 in Ask the GATK team
Hi, I am doing CNV somatic detection in exomes, and in the step of CollectAllelicCounts, it ask for an interval file, and says "The tool requires one or more genomic intervals specified with -L. The intervals can be either a Picard-style intervals list or a VCF. See Article#1109 for descriptions of formats. The sites should represent sites of common and/or sample-specific germline variant SNPs-only sites. Omit indel-type and mixed-variant-type sites."

Does that imply that for CNV detection is necessary to have done previously germline variant calling in the normal bam? So, do I have to do it?

Thank you very much

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  • afzmafzm Member
    Thank you for replying Bhanu, and sorry for questioning to much, but by "case and control" do you mean tumor and normal samples? And about the interval list provided, I do not understand what kind of sites should it represent (SNPs of a database, SNPs that are common to all of the samples used to build the Panel of Normals...)?

    Thank you
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