Somatic Purity & Ploidy Estimate

Implementation of purity and ploidy checking for somatic NGS samples

Default Configuration

The default configuration is as follows.

step_config:
  somatic_purity_ploidy_estimate:
    tools: ['ascat']  # REQUIRED - available: 'ascat'
    tool_cnv_calling: cnvetti
    # Configuration with read mapper and path to mapping output. Will use this
    # for generating a pileup using samtools for obtaining the b allele
    # fraction and computing coverage.
    tool_ngs_mapping: bwa
    path_ngs_mapping: ../ngs_mapping
    # Configuration of ASCAT method.
    ascat:
      # BED file with loci for B allele frequency.
      b_af_loci: REQUIRED  # REQUIRED