README.md

mutect

Summary

This pipeline calls somatic variants with Mutect (version 1; see paper and homepage)

The following steps are performed:

• Read mapping (see cfg/references.yaml for references used by default and also refer to option --references-cfg)
• Duplicate marking with sambamba (after merging if necessary)
• Indel Realignment with GATK (targets inferred from normal and tumor samples)
• Base quality recalibration with GATK, unless sequencing type is "targeted"
• Calling of somatic variants with Mutect. By default a contamination level of 2% is used.

Output

• Recalibrated BAM files for normal and tumor in the correspondly named subfolders
• Mutect results can be found in the variants subfolder. The most important are
  • mutect.txt.gz: Mutect's extended output
  • mutect.wig.gz: Coverage data
  • mutect.vcf.gz: All variants (annotated: mutect.snpeff.vcf.gz)
  • mutect.PASS.vcf.gz: Only passed variants (annotated: mutect.PASS.snpeff.vcf.gz)