config.yml

exe_root: "/topmed_variant_calling"
input_expression: "input/{sample_id}.cram"
batch_size: 1000
region_size: 10000000
merge_region_size: 100000
thresholds:
  vb_depth: 15
  freemix: 0.1
  frac_dp10: 0.9
contigs:
  chr1: 248956422
  chr2: 242193529
  chr3: 198295559
  chr4: 190214555
  chr5: 181538259
  chr6: 170805979
  chr7: 159345973
  chr8: 145138636
  chr9: 138394717
  chr10: 133797422
  chr11: 135086622
  chr12: 133275309
  chr13: 114364328
  chr14: 107043718
  chr15: 101991189
  chr16: 90338345
  chr17: 83257441
  chr18: 80373285
  chr19: 58617616
  chr20: 64444167
  chr21: 46709983
  chr22: 50818468
  chrX: 156040895
  chrY: 57227415
  chrM: 16569
autosome_contigs: [chr1, chr2, chr3, chr4, chr5, chr6, chr7, chr8, chr9, chr10, chr11, chr12, chr13, chr14, chr15, chr16, chr17, chr18, chr19, chr20, chr21, chr22]
sample_ids:
  - "HG00096"
  - "HG00097"
  - "HG00099"