Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.

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?

-Eric

Post edited by ekofman on

Best Answer

Answers

Sign In or Register to comment.