ACCESS_variant_calling_parameters.yaml

ACCESS_variant_calling_parameters.yaml

# Params
mutect_params:
  dcov: 5000
  read_filter: ['BadCigar']
  fraction_contamination: 0.0005
  minimum_mutation_cell_fraction: 0.0005

vardict_params:
  allele_freq_thres: 0.0005
  min_num_variant_reads: 1
  column_for_region_end: 3
  column_for_chromosome: 1
  column_for_gene_name: 4
  column_for_region_start: 2

basicfiltering_mutect_params:
  total_depth: 20
  allele_depth: 1
  variant_fraction: 0.00005
  tumor_normal_ratio: 1
  outdir: .

basicfiltering_vardict_params:
  min_qual: 0
  total_depth: 20
  allele_depth: 1
  tumor_normal_ratio: 1
  filter_germline: false
  variant_fraction: 0.00005
  outdir: .

bcftools_params:
  allow_overlaps: true
  rm_dups: all

vcf2maf_params:
  vep_forks: 4
  buffer_size: 5000
  max_filter_ac: 10
  min_hom_vaf: 0.7
  ncbi_build: GRCh37
  retain_info: 'set,TYPE,FAILURE_REASON,MUTECT,VCF_POS,VCF_REF,VCF_ALT'
  maf_center: mskcc.org
  species: homo_sapiens_merged

gbcms_params:
  maq: 20
  thread: 10
  omaf: true
  fragment_count: 1
  filter_duplicate: 0

access_filters_params:
  tumor_TD_min: 20 # Tumor Min Depth
  normal_TD_min: 20 # Normal Min Depth
  tn_ratio_thres: 2 # Tumor Normal Ratio threshold 
  tier_one_alt_min: 3
  tier_two_alt_min: 5
  tumor_detect_alt_thres: 2
  curated_detect_alt_thres: 2
  DS_tumor_detect_alt_thres: 2 # Duplex Simplex alt allele threshold
  DS_curated_detect_alt_thres: 2 # Duplex Simplex Curated alt allele threshold
  tumor_vaf_germline_thres: 0
  normal_vaf_germline_thres: 0.3
  min_n_curated_samples_alt_detected: 2