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