.command.out - Workdir - NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)

File Info

Filename: .command.out
Full Path: s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c9/cb4f5b94e096005f6193a6d1fc9087/.command.out
Size: 498 bytes
Task: NFCORE_HARMONIZE:HARMONIZE:HARMONIZE_SV:HARMONIZE_SV_ALTERA_INHOUSE_DNA:MANTA_SV_NORMALIZE (FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)
Attempt

Content

Parsing Manta VCF: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.manta.somatic_sv_custom.ann_snpEff_VEP.ann.vcf.gz
  Found 332 SV records
  TSV written to: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz.tsv
  BEDPE written to: FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1.sv.hmnz.bedpe
  SV type counts: {'DEL': 240, 'DUP': 29, 'INS': 23, 'BND': 40}
  Records with gene1 annotation: 332/332