Loading hotspot definitions from hotspot_definitions.tsv
  Loaded hotspot regions for 11 chromosomes (73 intervals)
Loading PON positions from pon_tnseq_42_curated_v4.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for 'pon_tnseq_42_curated_v4.vcf.gz'
  Loaded 550680 PON positions
Loading POT positions from aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz
[E::idx_find_and_load] Could not retrieve index file for 'aih_tumor_1577_pot_1pct_artifacts_only.vcf.gz'
  Loaded 545 POT positions
Loading BED files
Computing callable region (exome ∩ truth_panel - blacklist)
  Callable region: 9114 intervals across 23 chromosomes
Extracting variants from 869_B0C.norm.vcf.gz (mode=truth)
[E::idx_find_and_load] Could not retrieve index file for '869_B0C.norm.vcf.gz'
  Single sample: 869_B0C-T1-TDNA-1_HGJ2WDRX7_1_dna
Wrote 245 variants to 869_B0C.variants.tsv