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Panel of Normals

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sprokopec edited this page Jul 7, 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

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 (as of July 7 2021, these all use WXS data); if you have data that you would like to add to update these, please contact sprokopec.
  • alternatively, a panel generated using the 1000g cohort is also available
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