Loading hotspot definitions from hotspot_definitions.tsv
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
Opening reference FASTA Homo_sapiens_assembly38.fasta
Extracting variants from 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.filtered.vcf.gz (mode=test)
[E::idx_find_and_load] Could not retrieve index file for '1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.filtered.vcf.gz'
  VEP CSQ header found with 26 fields
  Samples: tumor=1029_0DT-T1-TDNA-1_23K7YCLT4_1 (idx=0), normal=1029_0DT-N1-BDNA-1_235YY7LT3_1 (idx=1)
Wrote 27988 variants to 1029_0DT-T1-TDNA-1_23K7YCLT4_1_vs_1029_0DT-N1-BDNA-1_235YY7LT3_1.variants.tsv