Skip to content

Panel of Normals

Jump to bottom
sprokopec edited this page Oct 21, 2021 · 2 revisions

Panel of Normals for SNV callers

Whenever possible, variant callers will generate a panel of normals to use for variant filtering. Depending on the tool, these panels list probable germline variants and/or sequencing artefacts.

  • MuTect: germline variants and sequencing artefacts, called using --artifact_detection_mode; is applied to all samples
  • Mutect2: germline variants and sequencing artefacts, called using --artifact_detection_mode; is applied to all samples
  • Strelka: germline variants, called using Strelka's germline workflow; applied to all tumour samples
  • VarScan: germline variants as determined by VarScan's processSomatic function; only applied to tumour-only samples
  • VarDict: germline variants as determined by VarDict; only applied to tumour-only samples

MuTect, Mutect2 and Strelka will produce a PoN ONLY if requested (using the --create-panel-of-normals argument) and therefore need to be run twice (once using the --create-panel-of-normals argument [this will process all available normals and produce the PoN] and then again without [to process all tumour samples, using the PoN]). VarScan and VarDict however will create these automatically during the course of the pipeline (so it only needs to be run once). See this wiki entry for more details on how to run the pipelines.

If desired, or, if matched normals are not available for your dataset, there are some pre-made panels available on H4H: /cluster/projects/pughlab/references/panel_of_normals

  • tool specific panels were developed using data output by this pipeline (both WXS and WGS options); if you have data that you would like to add to these, please contact sprokopec.
  • alternatively, a panel generated using the 1000g cohort is also available
Clone this wiki locally