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:                                            # Options: 'ascat'
    #  - ascat
    #
    # When set to 'copywriter', will trigger 'somatic_targeted_seq_cnv_calling'
    #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
    #path_somatic_targeted_seq_cnv_calling: ''
    #ascat:
    #
    #  # BED file with loci for B allele frequency.
    #  b_af_loci:                                      # REQUIRED