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