Results are split by patient and therein by sample(s). Each sample folder contains the raw outputs from the various typing tools. Usable reports are stored under Reports in JSON and PDF format.
The JSON format can be used to programmatically parse and transform the result data. An example follows below. A few gottchas:
- Exon names are given in their GenCode 42 designation.
- mean_cov really is the mean coverage over an exon, irrespective of its length (duh). So the number tells you nothing about whether coverage is partial or complete.
{
"sample": "HG0001",
"coverage": {
"HLA-A": [{
"exon": "HLA-A.ENST00000376809.1",
"seq": "chr6",
"start": 29942554,
"stop": 29942626,
"strand": "+",
"mean_cov": 33
}, {
"exon": "HLA-A.ENST00000376809.2",
"seq": "chr6",
"start": 29942757,
"stop": 29943026,
"strand": "+",
"mean_cov": 42
}, {
"exon": "HLA-A.ENST00000376809.3",
"seq": "chr6",
"start": 29943268,
"stop": 29943543,
"strand": "+",
"mean_cov": 45
}, {
"exon": "HLA-A.ENST00000376809.4",
"seq": "chr6",
"start": 29944122,
"stop": 29944397,
"strand": "+",
"mean_cov": 51
}, {
"exon": "HLA-A.ENST00000376809.5",
"seq": "chr6",
"start": 29944500,
"stop": 29944616,
"strand": "+",
"mean_cov": 43
}, {
"exon": "HLA-A.ENST00000376809.6",
"seq": "chr6",
"start": 29945059,
"stop": 29945091,
"strand": "+",
"mean_cov": 55
}, {
"exon": "HLA-A.ENST00000376809.7",
"seq": "chr6",
"start": 29945234,
"stop": 29945281,
"strand": "+",
"mean_cov": 47
}, {
"exon": "HLA-A.ENST00000376809.8",
"seq": "chr6",
"start": 29945451,
"stop": 29945455,
"strand": "+",
"mean_cov": 54
}],
"HLA-B": [{
"exon": "HLA-B.ENST00000412585.1",
"seq": "chr6",
"start": 31357086,
"stop": 31357158,
"strand": "-",
"mean_cov": 41
}, {
"exon": "HLA-B.ENST00000412585.2",
"seq": "chr6",
"start": 31356688,
"stop": 31356957,
"strand": "-",
"mean_cov": 42
}, {
"exon": "HLA-B.ENST00000412585.3",
"seq": "chr6",
"start": 31356167,
"stop": 31356442,
"strand": "-",
"mean_cov": 33
}, {
"exon": "HLA-B.ENST00000412585.4",
"seq": "chr6",
"start": 31355317,
"stop": 31355592,
"strand": "-",
"mean_cov": 62
}, {
"exon": "HLA-B.ENST00000412585.5",
"seq": "chr6",
"start": 31355107,
"stop": 31355223,
"strand": "-",
"mean_cov": 43
}, {
"exon": "HLA-B.ENST00000412585.6",
"seq": "chr6",
"start": 31354633,
"stop": 31354665,
"strand": "-",
"mean_cov": 36
}, {
"exon": "HLA-B.ENST00000412585.7",
"seq": "chr6",
"start": 31354483,
"stop": 31354526,
"strand": "-",
"mean_cov": 29
}],
"HLA-C": [{
"exon": "HLA-C.ENST00000376228.1",
"seq": "chr6",
"start": 31271999,
"stop": 31272071,
"strand": "-",
"mean_cov": 35
}, {
"exon": "HLA-C.ENST00000376228.2",
"seq": "chr6",
"start": 31271599,
"stop": 31271868,
"strand": "-",
"mean_cov": 36
}, {
"exon": "HLA-C.ENST00000376228.3",
"seq": "chr6",
"start": 31271073,
"stop": 31271348,
"strand": "-",
"mean_cov": 49
}, {
"exon": "HLA-C.ENST00000376228.4",
"seq": "chr6",
"start": 31270210,
"stop": 31270485,
"strand": "-",
"mean_cov": 42
}, {
"exon": "HLA-C.ENST00000376228.5",
"seq": "chr6",
"start": 31269966,
"stop": 31270085,
"strand": "-",
"mean_cov": 36
}, {
"exon": "HLA-C.ENST00000376228.6",
"seq": "chr6",
"start": 31269493,
"stop": 31269525,
"strand": "-",
"mean_cov": 47
}, {
"exon": "HLA-C.ENST00000376228.7",
"seq": "chr6",
"start": 31269338,
"stop": 31269385,
"strand": "-",
"mean_cov": 37
}, {
"exon": "HLA-C.ENST00000376228.8",
"seq": "chr6",
"start": 31269169,
"stop": 31269173,
"strand": "-",
"mean_cov": 30
}],
"HLA-DRB1": [{
"exon": "HLA-DRB1.ENST00000360004.1",
"seq": "chr6",
"start": 32589643,
"stop": 32589742,
"strand": "-",
"mean_cov": 65
}, {
"exon": "HLA-DRB1.ENST00000360004.2",
"seq": "chr6",
"start": 32584109,
"stop": 32584378,
"strand": "-",
"mean_cov": 47
}, {
"exon": "HLA-DRB1.ENST00000360004.3",
"seq": "chr6",
"start": 32581557,
"stop": 32581838,
"strand": "-",
"mean_cov": 51
}, {
"exon": "HLA-DRB1.ENST00000360004.4",
"seq": "chr6",
"start": 32580746,
"stop": 32580856,
"strand": "-",
"mean_cov": 79
}, {
"exon": "HLA-DRB1.ENST00000360004.5",
"seq": "chr6",
"start": 32580247,
"stop": 32580270,
"strand": "-",
"mean_cov": 85
}, {
"exon": "HLA-DRB1.ENST00000360004.6",
"seq": "chr6",
"start": 32579091,
"stop": 32579104,
"strand": "-",
"mean_cov": 73
}],
"HLA-DQA1": [{
"exon": "HLA-DQA1.ENST00000343139.1",
"seq": "chr6",
"start": 32637459,
"stop": 32637540,
"strand": "+",
"mean_cov": 48
}, {
"exon": "HLA-DQA1.ENST00000343139.2",
"seq": "chr6",
"start": 32641310,
"stop": 32641558,
"strand": "+",
"mean_cov": 37
}, {
"exon": "HLA-DQA1.ENST00000343139.3",
"seq": "chr6",
"start": 32641972,
"stop": 32642253,
"strand": "+",
"mean_cov": 44
}, {
"exon": "HLA-DQA1.ENST00000343139.4",
"seq": "chr6",
"start": 32642610,
"stop": 32642764,
"strand": "+",
"mean_cov": 35
}],
"HLA-DQB1": [{
"exon": "HLA-DQB1.ENST00000434651.1",
"seq": "chr6",
"start": 32666499,
"stop": 32666607,
"strand": "-",
"mean_cov": 47
}, {
"exon": "HLA-DQB1.ENST00000434651.2",
"seq": "chr6",
"start": 32664798,
"stop": 32665067,
"strand": "-",
"mean_cov": 30
}, {
"exon": "HLA-DQB1.ENST00000434651.3",
"seq": "chr6",
"start": 32661967,
"stop": 32662248,
"strand": "-",
"mean_cov": 43
}, {
"exon": "HLA-DQB1.ENST00000434651.4",
"seq": "chr6",
"start": 32661347,
"stop": 32661457,
"strand": "-",
"mean_cov": 44
}, {
"exon": "HLA-DQB1.ENST00000434651.5",
"seq": "chr6",
"start": 32660236,
"stop": 32660249,
"strand": "-",
"mean_cov": 52
}],
"HLA-DPA1": [{
"exon": "HLA-DPA1.ENST00000419277.2",
"seq": "chr6",
"start": 33073471,
"stop": 33073570,
"strand": "-",
"mean_cov": 46
}, {
"exon": "HLA-DPA1.ENST00000419277.3",
"seq": "chr6",
"start": 33069641,
"stop": 33069886,
"strand": "-",
"mean_cov": 60
}, {
"exon": "HLA-DPA1.ENST00000419277.4",
"seq": "chr6",
"start": 33069019,
"stop": 33069300,
"strand": "-",
"mean_cov": 46
}, {
"exon": "HLA-DPA1.ENST00000419277.5",
"seq": "chr6",
"start": 33068650,
"stop": 33068804,
"strand": "-",
"mean_cov": 56
}],
"HLA-DPB1": [{
"exon": "HLA-DPB1.ENST00000418931.1",
"seq": "chr6",
"start": 33076042,
"stop": 33076141,
"strand": "+",
"mean_cov": 69
}, {
"exon": "HLA-DPB1.ENST00000418931.2",
"seq": "chr6",
"start": 33080672,
"stop": 33080935,
"strand": "+",
"mean_cov": 35
}, {
"exon": "HLA-DPB1.ENST00000418931.3",
"seq": "chr6",
"start": 33084950,
"stop": 33085231,
"strand": "+",
"mean_cov": 55
}, {
"exon": "HLA-DPB1.ENST00000418931.4",
"seq": "chr6",
"start": 33085779,
"stop": 33085889,
"strand": "+",
"mean_cov": 49
}, {
"exon": "HLA-DPB1.ENST00000418931.5",
"seq": "chr6",
"start": 33086219,
"stop": 33086238,
"strand": "+",
"mean_cov": 67
}]
},
"calls": {
"A": {
"HLA-HD": ["11:01", "01:01"],
"xHLA": ["01:01", "11:01"],
"HLAscan": ["01:01", "11:01"],
"Optitype": ["01:01", "11:01"],
"Hisat": ["11:01 (0.5131)", "01:01 (0.4869)"]
},
"B": {
"HLA-HD": ["56:01", "08:01"],
"xHLA": ["08:01", "56:01"],
"HLAscan": ["08:01", "56:01"],
"Optitype": ["08:01", "56:01"],
"Hisat": ["08:01 (0.5101)", "56:01 (0.4898)"]
},
"C": {
"HLA-HD": ["01:02", "07:01"],
"xHLA": ["01:02", "07:01"],
"HLAscan": ["07:01", "01:02"],
"Optitype": ["01:02", "07:01"],
"Hisat": ["07:01 (0.5046)", "01:02 (0.4954)"]
},
"DQB1": {
"HLA-HD": ["02:01", "05:01"],
"xHLA": ["02:01", "05:01"],
"HLAscan": ["05:01", "02:01"],
"Optitype": [],
"Hisat": ["02:01 (0.5037)", "05:01 (0.4963)"]
},
"DRB1": {
"HLA-HD": ["03:01", "01:01"],
"xHLA": ["01:01", "03:01"],
"HLAscan": ["03:01", "01:01"],
"Optitype": [],
"Hisat": ["01:01 (0.4159)", "03:01 (0.3597)"]
},
"DRB4": {
"HLA-HD": [],
"xHLA": [],
"HLAscan": [],
"Optitype": [],
"Hisat": []
},
"DRB5": {
"HLA-HD": [],
"xHLA": [],
"HLAscan": [],
"Optitype": [],
"Hisat": []
},
"DQA1": {
"HLA-HD": ["01:01", "05:01"],
"xHLA": [],
"HLAscan": ["01:05", "05:01"],
"Optitype": [],
"Hisat": ["01:01 (0.5107)", "05:01 (0.4893)"]
},
"DRB3": {
"HLA-HD": ["01:01"],
"xHLA": [],
"HLAscan": [],
"Optitype": [],
"Hisat": []
},
"DPA1": {
"HLA-HD": ["01:03", "02:01"],
"xHLA": [],
"HLAscan": ["01:03", "02:01"],
"Optitype": [],
"Hisat": ["02:01 (0.5554)", "01:03 (0.4445)"]
},
"DPB1": {
"HLA-HD": ["14:01", "04:01"],
"xHLA": ["04:01", "14:01"],
"HLAscan": ["04:01", "14:01"],
"Optitype": [],
"Hisat": ["14:01 (0.5354)", "04:01 (0.3981)"]
}
},
"pipeline_version": "1.5rc1",
"date": "18.07.2023",
"commercial_tools": ["HLA-HD", "xHLA", "HLAscan"]
}