File Info

Filename
FFPE_HD789_01_p1_gDNA_0005_B23KKT2LT4_1_vs_NA12878_c_0003_gDNA_0002_A237CFYLT3_1.summary.json
Full Path
s3://natera-platform-sandbox/platform-users/sgreer/projects/A15_hmz_test/aih_dna/FFPE_HD789_01_p1_gDNA_0005_B23KKT2LT4_1_vs_NA12878_c_0003_gDNA_0002_A237CFYLT3_1/FFPE_HD789_01_p1_gDNA_0005_B23KKT2LT4_1_vs_NA12878_c_0003_gDNA_0002_A237CFYLT3_1.summary.json
Size
2.9 KB
Workflow Run
aih-dna-test-198bb41c
Published
Mar 01, 2026 12:05 PM
{
  "sequencing_library_id": "FFPE_HD789_01_p1_gDNA_0005_B23KKT2LT4_1",
  "secondary_sequencing_library_id": "NA12878_c_0003_gDNA_0002_A237CFYLT3_1",
  "data_source": "altera_inhouse_dna",
  "harmonized_software_version": "198bb41c7021831bbb85b464458aae3d09416b97",
  "software_version": "2418a8b1c2ce0891ab655d4699cb6f795c84298a",
  "harmonized_s3_path": "s3://natera-platform-sandbox/platform-users/sgreer/projects/A15_hmz_test/aih_dna",
  "s3_path": "s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/tools__2418a8b1--20260217-172825",
  "s3_path_params": "s3://natera-platform-sandbox/pipeline-outputs/cgp_runs/nextflow/cgp_dna_exp0024/tools__2418a8b1--20260217-172825/pipeline_info/params_2026-02-17_17-33-00.json",
  "s3_path_qc": null,
  "altera_exact_report_details": null,
  "qc": {
    "calculated_sex": "XX",
    "calculated_sex_secondary": "XX",
    "tumor_normal_correlation": 0.5134,
    "tumor_contamination": 59.747,
    "normal_contamination": 0.041,
    "tso500_wetlab_pass": null,
    "tso500_seq_pass": null
  },
  "harmonized_input_file_status": {
    "snv_somatic": true,
    "snv_somatic_phased": true,
    "snv_germline": true,
    "cnv": true,
    "sv": true,
    "fusion": false,
    "splice": false,
    "tmb": true,
    "msi": true,
    "hrd_scarhrd": true,
    "hrd_tih": true,
    "hla": true,
    "chip": true
  },
  "harmonized_summary_stats": {
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    "somatic_sv_fusion_actionable_num": 2,
    "chip_variant_num": 12545,
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    "germline_cnv_hrr_num": null,
    "tumor_purity": 0.53608890946128,
    "tumor_ploidy": 2.09811974851314,
    "scarhrd_score": 35.0,
    "scarhrd_status": "HRD_neg",
    "tih_hrd_score": 96.0,
    "tih_hrd_status": "HRD_pos",
    "tso500_gis": null,
    "tso500_hrd_status": null,
    "msi_status": "MSI-L",
    "msi_score": 46.32,
    "tmb_status": "LOW",
    "tmb_score": 0.0293,
    "rna_fusion_total_num": null,
    "rna_fusion_filtered_num": null,
    "tso500_overlap_rna_fusion_total_num": null,
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    "rna_fusion_filtered_and_actionable_num": null,
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    "rna_exon_skipping_total_num": null,
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    "tso500_overlap_somatic_snv_num": 1414,
    "tso500_overlap_somatic_indel_num": 137,
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    "tso500_overlap_somatic_cnv_num": 128,
    "tso500_overlap_somatic_cnv_del_num": 50,
    "tso500_overlap_somatic_cnv_amp_num": 78
  }
}