# Default filter settings for mode: ctDNA
# these generally won't have normals, but include filters anyways
#
# Filters supplied under default are used as the baseline for all callers
# any filters specified under a specific caller will take precedence over
# the default filters
filters:
  default:
    min_tumour_variant_reads: 5
    min_tumour_allele_frequency: 0.01
    ct_min_tumour_allele_frequency: 0.05
    indel_min_tumour_allele_frequency: 0.05
    min_normal_depth: 5
    max_normal_allele_frequency: 0
    remove_1000_genomes: true
    remove_exac: true
  pgm:
    indel_min_tumour_allele_frequency: 0.02
  vardict:
    remove_germline_status: true
  isis:
    indel_min_tumour_allele_frequency: 0.02
