GIS JSON Full

{
    "startTime": "Thu Aug 24 02:18:17 2023",
    "options": {
        "pon": "\/opt\/edico\/resources\/PhenoHRD\/pon.json.gz",
        "nEv": "15",
        "min-coverage-tso": "1",
        "min-coverage-hrd": "1",
        "min-coverage-snp": "40",
        "min-align-quality": "30",
        "min-phred-score": "30",
        "probes": "\/opt\/edico\/resources\/PhenoHRD\/Probes.vcf.gz",
        "max-noise-frac": "0.029999999329447746",
        "input-dialect": "bam",
        "is-tumor": "true",
        "hmm-Z": "19",
        "input-file": "28_DNA_Mixed_Training_rep1.bam",
        "output-directory": "Gis",
        "threads": "8",
        "annotate-tso-cnv": "true",
        "annotate-tso-cnv-in": "28_DNA_Mixed_Training_rep1.cnv.vcf.gz",
        "annotate-tso-genes": "true",
        "annotate-tso-bed-in": "resource_bundle\/cnv\/TSO500_gene_shapes.bed",
        "genome-abcn": "false"
    },
    "version": "PhenoHRD  1.0.4 release (compiled: Aug 16 2023 21:42:58)",
    "input": "28_DNA_Mixed_Training_rep1.bam",
    "CNV": {
        "qc": {
            "bCorrelationPre": "0.12452248860469835",
            "bCorrelationPost": "0.023519456708157225",
            "sex": "Female",
            "coverage": {
                "ALL": {
                    "median": "87",
                    "mad": "33",
                    "total_mtc": "87",
                    ">30": "94.9657288",
                    ">50": "82.4426956",
                    ">75": "61.1827736",
                    ">100": "41.7508163",
                    "totalProbes": "43407",
                    "passQcProbes": "40701",
                    "dosageMMAD": "0.22526039404870163"
                },
                "HRD": {
                    "median": "72",
                    "mad": "26",
                    "total_mtc": "72",
                    ">30": "92.3798828",
                    ">50": "75.2540741",
                    ">75": "48.4582443",
                    ">100": "26.9817924",
                    "totalProbes": "25227",
                    "passQcProbes": "23123",
                    "dosageMMAD": "0.23774177313485834"
                },
                "TSO": {
                    "median": "115",
                    "mad": "41",
                    "total_mtc": "115",
                    ">75": "77.9212646",
                    ">100": "61.1787453",
                    ">125": "44.5443153",
                    ">150": "31.4597797",
                    "totalProbes": "18180",
                    "passQcProbes": "17578",
                    "dosageMMAD": "0.22374418113286099"
                }
            }
        }
    },
    "MYRIAD": {
        "executed": "true",
        "excessiveTF": "0",
        "score": {
            "GIS": "64",
            "amplification": "1.96",
            "contamination": "0.23000000000000001"
        },
        "HMM_iterations": "20",
        "qc": {
            "alleleDosageChange": "0.18177843862221937",
            "alleleDosageNoise": "0.06663797786238973",
            "alleleDosageRatio": "0.36658901004689537",
            "bAlleleBias": "-0.011008473389601259"
        }
    },
    "sample-qc": "PASS",
    "stopTime": "Thu Aug 24 02:19:51 2023"
}