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TMB, MSI, GIS Input Requirement

Tumor Mutational Burden (TMB)

File Type

Sample File Name

Examples

JSON

*.tmb.json

Microsatellite Instability (MSI)

File Type

Sample File Name

Examples

Genomic Instability Score (GIS)

File Type

Sample File Name

Examples

Homologous Recombination Deficiency Score (HRD)

File Type

Sample File Name

Examples

Human Leukocyte Antigen Genotype (HLA)

File Type

Sample File Name

Examples

TMB JSON Minimal

{
    "TmbPerMb": 3.14823318
}

TMB JSON Full

TMB CSV Minimal

TMB SUMMARY,,TMB,3.36

TMB CSV Full

TMB SUMMARY,,Total Input Variant Count,1381
TMB SUMMARY,,Total Input Variant Count in TMB region,500
TMB SUMMARY,,Filtered Variant Count,4
TMB SUMMARY,,Filtered Nonsyn Variant Count,3
TMB SUMMARY,,Eligible Region (MB),1.19
TMB SUMMARY,,TMB,3.36
TMB SUMMARY,,Nonsyn TMB,2.52

MSI JSON Minimal

{
    "PercentageUnstableSites": "1.3",
    "SumDistance": "0.20699999999999999"
}

MSI JSON Full

{
    "Settings": {
        "Command": "tumor-only",
        "MicrosatelliteFilePath": "resource_bundle\/msi\/references\/microsatellites-TSO500-SOLID-concordant.list",
        "RefereceNormalDirectory": "resource_bundle\/msi\/data\/TSO500-Solid",
        "FilterReferenceAllele": "false",
        "FilterDuplexReads": "false",
        "MinHomopolymerAllele": "5",
        "PValueThreshold": "0.01",
        "DistanceThreshold": "0.10000000149011612",
        "SpanningCoverageThreshold": "60",
        "DistanceSignDependsOnDensityDifference": "false",
        "MinReferencePeakHeight": "0",
        "MinLeftPeakHeight": "0",
        "MinLeftPeakRatio": "0",
        "MaxLeftPeakRatio": "3.40282347e+38",
        "OutputDirectory": "DnaDragenCaller",
        "OutputPrefix": "28_DNA_Mixed_Training_rep1"
    },
    "TotalMicrosatelliteSitesAssessed": "77",
    "TotalMicrosatelliteSitesUnstable": "1",
    "PercentageUnstableSites": "1.3",
    "ResultIsValid": "true",
    "ResultMessage": "",
    "SumDistance": "0.20699999999999999"
}

GIS JSON Minimal

GIS JSON Full

HRD CSV Full

HLA TSV Full

gene    num_alleles     allele_1        reads_supporting_allele_1       EM_posterior_allele_1   allele_2        reads_supporting_allele_2       EM_posterior_allele_2   Notes
A       1       A*32:01 1227    1.000000        NA      NA      NA      NA
B       1       B*15:01 1158    1.000000        NA      NA      NA      NA
C       2       C*03:03 1361    0.770833        C*03:04 1310    0.229167        NA
DMA     1       DMA*01:01       1833    1.000000        NA      NA      NA      NA
DMB     1       DMB*01:01       2247    0.975507        NA      NA      NA      NA
DOA     1       DOA*01:01       1497    1.000000        NA      NA      NA      NA
DOB     1       DOB*01:01       1769    1.000000        NA      NA      NA      NA
DPA1    1       DPA1*01:03      3411    1.000000        NA      NA      NA      NA
DPA2    2       DPA2*01:01      2560    0.562016        DPA2*02:01      2528    0.437984        NA
DPB1    2       DPB1*02:01      4360    0.443701        DPB1*31:01      3013    0.151119        NA
DPB2    2       DPB2*01:01      5734    0.749003        DPB2*03:01      3784    0.242016        NA
DQA1    2       DQA1*01:01      1869    0.740983        DQA1*06:01      603     0.225755        NA
DQA2    1       DQA2*01:01      2301    0.988328        NA      NA      NA      NA
DQB1    2       DQB1*05:01      2129    0.751502        DQB1*03:01      719     0.248498        NA
DQB2    1       DQB2*01:01      2768    1.000000        NA      NA      NA      NA
DRA     2       DRA*01:01       1876    0.814725        DRA*01:03       1098    0.185275        NA
DRB1    2       DRB1*01:01      779     0.731210        DRB1*08:03      290     0.171451        NA
DRB5    2       DRB5*02:02      49      0.608936        DRB5*02:21      33      0.291917        Allele1:LowSupportingReads Allele2:LowSupportingReads
E       2       E*01:03 1402    0.793814        E*01:01 1345    0.206186        NA
F       1       F*01:01 1420    1.000000        NA      NA      NA      NA
G       1       G*01:01 1361    0.971827        NA      NA      NA      NA
H       1       H*02:03 1386    1.000000        NA      NA      NA      NA
J       1       J*01:01 1526    0.998765        NA      NA      NA      NA
K       1       K*01:01 1403    0.990965        NA      NA      NA      NA
L       1       L*01:01 1378    0.996270        NA      NA      NA      NA
N       1       N*01:01 209     1.000000        NA      NA      NA      NA
P       1       P*02:01 1192    0.999039        NA      NA      NA      NA
S       2       S*01:04 314     0.809390        S*01:02 183     0.153795        NA
T       1       T*02:01 919     0.956639        NA      NA      NA      NA
U       2       U*01:02 208     0.721489        U*01:03 71      0.215357        NA
V       1       V*01:01 794     1.000000        NA      NA      NA      NA
W       2       W*04:01 1026    0.825142        W*02:01 664     0.168624        NA
MICA    1       MICA*010:01     5188    1.000000        NA      NA      NA      NA
MICB    2       MICB*005:02     4603    0.630347        MICB*019:01     4283    0.298161        NA
TAP1    1       TAP1*01:01      3380    0.999999        NA      NA      NA      NA
TAP2    2       TAP2*02:01      3481    0.544792        TAP2*01:01      3308    0.374378        NA
HFE     1       HFE*001:01      3       1.000000        NA      NA      NA      Allele1:LowSupportingReads
DRB3    0       NA      NA      NA      NA      NA      NA      NA
DRB4    1       DRB4*01:183     20      0.125000        NA      NA      NA      Allele1:LowSupportingReads
Y       0       NA      NA      NA      NA      NA      NA      NA
R       0       NA      NA      NA      NA      NA      NA      NA

{
    "TmbPerMb": 3.14823318,
    "AdjustedTmbPerMb": 3.14823318,
    "NonsynonymousTmbPerMb": 3.14823318,
    "AdjustedNonsynonymousTmbPerMb": 3.14823318,
    "SomaticCodingVariantsCount": 4,
    "NonsynonymousSomaticCodingVariantsCount": 4,
    "TotalRegionSizeMb": 1.881725,
    "CodingRegionSizeMb": 1.270554,
    "Settings": {
        "JsonPath": "/opt/illumina/analysis-folder/Logs_Intermediates/Annotation/SeraCare-TriLevelv2-DNA/SeraCare-TriLevelv2-DNA_DNAVariantsTMB_Annotated.json.gz",
        "TmbInputRegions": "/opt/illumina/analysis-folder/Logs_Intermediates/SmallVariantFilter/SeraCare-TriLevelv2-DNA/SeraCare-TriLevelv2-DNA_SmallVariants.genome.vcf",
        "IncludedRegions": "/opt/illumina/resources/Refseq.CodingRegions.hg19.bed",
        "ExcludedRegions": "/opt/illumina/resources/pepe2/pepe_blacklist.bed",
        "OutputDir": "/opt/illumina/analysis-folder/Logs_Intermediates/Tmb/SeraCare-TriLevelv2-DNA",
        "LowerVafThreshold": 0.05,
        "UpperVafThreshold": 1.0,
        "CosmicDriverThreshold": 50,
        "VariantTypes": ["SNV","deletion","insertion"],
        "DepthThreshold": 50,
        "CorrectionSlope": 1.0,
        "CorrectionIntercept": 0.0,
        "SkipProxiFilter": false,
        "DbFilterThreshold": 10
    }
}

HLA TSV Full

gene    num_alleles     allele_1        reads_supporting_allele_1       EM_posterior_allele_1   allele_2        reads_supporting_allele_2       EM_posterior_allele_2   Notes
A       1       A*32:01 1227    1.000000        NA      NA      NA      NA
B       1       B*15:01 1158    1.000000        NA      NA      NA      NA
C       2       C*03:03 1361    0.770833        C*03:04 1310    0.229167        NA
DMA     1       DMA*01:01       1833    1.000000        NA      NA      NA      NA
DMB     1       DMB*01:01       2247    0.975507        NA      NA      NA      NA
DOA     1       DOA*01:01       1497    1.000000        NA      NA      NA      NA
DOB     1       DOB*01:01       1769    1.000000        NA      NA      NA      NA
DPA1    1       DPA1*01:03      3411    1.000000        NA      NA      NA      NA
DPA2    2       DPA2*01:01      2560    0.562016        DPA2*02:01      2528    0.437984        NA
DPB1    2       DPB1*02:01      4360    0.443701        DPB1*31:01      3013    0.151119        NA
DPB2    2       DPB2*01:01      5734    0.749003        DPB2*03:01      3784    0.242016        NA
DQA1    2       DQA1*01:01      1869    0.740983        DQA1*06:01      603     0.225755        NA
DQA2    1       DQA2*01:01      2301    0.988328        NA      NA      NA      NA
DQB1    2       DQB1*05:01      2129    0.751502        DQB1*03:01      719     0.248498        NA
DQB2    1       DQB2*01:01      2768    1.000000        NA      NA      NA      NA
DRA     2       DRA*01:01       1876    0.814725        DRA*01:03       1098    0.185275        NA
DRB1    2       DRB1*01:01      779     0.731210        DRB1*08:03      290     0.171451        NA
DRB5    2       DRB5*02:02      49      0.608936        DRB5*02:21      33      0.291917        Allele1:LowSupportingReads Allele2:LowSupportingReads
E       2       E*01:03 1402    0.793814        E*01:01 1345    0.206186        NA
F       1       F*01:01 1420    1.000000        NA      NA      NA      NA
G       1       G*01:01 1361    0.971827        NA      NA      NA      NA
H       1       H*02:03 1386    1.000000        NA      NA      NA      NA
J       1       J*01:01 1526    0.998765        NA      NA      NA      NA
K       1       K*01:01 1403    0.990965        NA      NA      NA      NA
L       1       L*01:01 1378    0.996270        NA      NA      NA      NA
N       1       N*01:01 209     1.000000        NA      NA      NA      NA
P       1       P*02:01 1192    0.999039        NA      NA      NA      NA
S       2       S*01:04 314     0.809390        S*01:02 183     0.153795        NA
T       1       T*02:01 919     0.956639        NA      NA      NA      NA
U       2       U*01:02 208     0.721489        U*01:03 71      0.215357        NA
V       1       V*01:01 794     1.000000        NA      NA      NA      NA
W       2       W*04:01 1026    0.825142        W*02:01 664     0.168624        NA
MICA    1       MICA*010:01     5188    1.000000        NA      NA      NA      NA
MICB    2       MICB*005:02     4603    0.630347        MICB*019:01     4283    0.298161        NA
TAP1    1       TAP1*01:01      3380    0.999999        NA      NA      NA      NA
TAP2    2       TAP2*02:01      3481    0.544792        TAP2*01:01      3308    0.374378        NA
HFE     1       HFE*001:01      3       1.000000        NA      NA      NA      Allele1:LowSupportingReads
DRB3    0       NA      NA      NA      NA      NA      NA      NA
DRB4    1       DRB4*01:183     20      0.125000        NA      NA      NA      Allele1:LowSupportingReads
Y       0       NA      NA      NA      NA      NA      NA      NA
R       0       NA      NA      NA      NA      NA      NA      NA

{
    "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"
}

{
    "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"
}

TMB, MSI, GIS Input Requirement

hashtagTumor Mutational Burden (TMB)

hashtagMicrosatellite Instability (MSI)

hashtagGenomic Instability Score (GIS)

hashtagHomologous Recombination Deficiency Score (HRD)

hashtagHuman Leukocyte Antigen Genotype (HLA)

TMB JSON Minimal

TMB JSON Full

TMB CSV Minimal

TMB CSV Full

MSI JSON Minimal

MSI JSON Full

GIS JSON Minimal

GIS JSON Full

HRD CSV Full

HLA TSV Full

MSI JSON Full

TMB, MSI, GIS Input Requirement

hashtagTumor Mutational Burden (TMB)

hashtagMicrosatellite Instability (MSI)

hashtagGenomic Instability Score (GIS)

hashtagHomologous Recombination Deficiency Score (HRD)

hashtagHuman Leukocyte Antigen Genotype (HLA)

TMB CSV Full

TMB JSON Full

GIS JSON Minimal

MSI JSON Minimal

TMB JSON Minimal

HRD CSV Full

TMB CSV Minimal

HLA TSV Full

GIS JSON Full

Tumor Mutational Burden (TMB)

Microsatellite Instability (MSI)

Genomic Instability Score (GIS)

Homologous Recombination Deficiency Score (HRD)

Human Leukocyte Antigen Genotype (HLA)

Tumor Mutational Burden (TMB)

Microsatellite Instability (MSI)

Genomic Instability Score (GIS)

Homologous Recombination Deficiency Score (HRD)

Human Leukocyte Antigen Genotype (HLA)