.command.out - Workdir - NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/e190033328843e631c5f248e5ea364/.command.out
Size: 466 bytes
Task: NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1)
Attempt

Content

Parsing Manta VCF: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 83 SV records
  TSV written to: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.tsv
  BEDPE written to: PX_FFPE_kid_nat_03_03_A23WJ5GLT4_2_vs_1136_85O-N1-BDNA-1_B23KGCJLT4_1.sv.hmnz.bedpe
  SV type counts: {'DEL': 20, 'BND': 50, 'DUP': 12, 'INS': 1}
  Records with gene1 annotation: 83/83