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CNVSomaticPairWorkflow DenoiseReadCountsNormal PoN Error

ekofmanekofman Member, Broadie
edited June 2018 in Ask the FireCloud Team

Hi, I'm running the CNVSomaticPair Workflow, and am using the gatk-recommended WGS panel of normals "cnv_somatic_PoN_4.0_WGS_for_public.pon.hdf5" which I found in the bucket https://console.cloud.google.com/storage/browser/gatk-test-data/cnv/somatic/.

Do you know what intervals were used in generating that PoN? Is there an WGS hg19/b37 interval list in that google bucket I might use instead to avoid receiving the following error?

java.lang.IllegalArgumentException: Sample intervals must be identical to the original intervals used to build the panel of normals

Thanks! @bshifaw as the author the FireCloud method perhaps you have an idea of the proper interval list?


Post edited by ekofman on

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