TinDaisy2 workflow v2.6

July 17, 2023 ยท View on GitHub

Description of parameters in TinDaisy2 v2.6 pipeline. See here for more general information about TinDaisy2.

Versions

  • v2.6.2 - Bugfix to VCF headers. Using updated VEP v99.
  • v2.6.1 - Adds bypass_classification parameter. Also introducing -ffpe variant
  • v2.6 Adding staging of BAMs. Does not affect results
  • v2.5 pipeline uses cwl/workflows/tindaisy2.cwl workflow

General filter parameters

  • For indels, require length < 100
  • Require normal VAF <= 0.02, tumor VAF >= 0.05 for all variants
  • Require read depth in tumor > 14 and normal > 8 for all variants
  • All variants must be called by 2 or more callers
  • Require Allele Frequency < 0.005 (as determined by vep)
  • Retain exonic calls
  • Exclude calls which are in dbSnP but not in COSMIC or ClinVar
  • Adjacent variants merged into DNP, TNP, and QNP

VAF Rescue is not used

Specific databases used

Output

Three files are output:

  • ProximityFiltered.vcf = Output VCF - contains all variants which were called by 2 or 3 callers.
    • The FILTER field of this VCF indicates which filters a variant failed, or PASS if passed all filters
  • result.maf = Clean VCF - contains only variants which passed all filters
  • HotspotFiltered.vcf = Clean MAF - MAF file corresponding to Clean VCF