forked from txje/population-ancestry-viewer
-
Notifications
You must be signed in to change notification settings - Fork 0
/
meta.json
113 lines (110 loc) · 4.66 KB
/
meta.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
{
"description": "1000 genomes Phase 1 MXL population chromosomes 21 and 22.<br/>Coordinates are on NCBI36/hg18.<br/><br/><i>An integrated map of genetic variation from 1092 human genomes</i>. Nature 491, 56–65 (01 November 2012) doi:10.1038/nature11632",
"samples": [
{"name": "NA19648", "set": "MXL"},
{"name": "NA19660", "set": "MXL"},
{"name": "NA19676", "set": "MXL"},
{"name": "NA19685", "set": "MXL"},
{"name": "NA19723", "set": "MXL"},
{"name": "NA19732", "set": "MXL"},
{"name": "NA19741", "set": "MXL"},
{"name": "NA19753", "set": "MXL"},
{"name": "NA19762", "set": "MXL"},
{"name": "NA19776", "set": "MXL"},
{"name": "NA19785", "set": "MXL"},
{"name": "NA19651", "set": "MXL"},
{"name": "NA19661", "set": "MXL"},
{"name": "NA19678", "set": "MXL"},
{"name": "NA19716", "set": "MXL"},
{"name": "NA19725", "set": "MXL"},
{"name": "NA19734", "set": "MXL"},
{"name": "NA19746", "set": "MXL"},
{"name": "NA19755", "set": "MXL"},
{"name": "NA19764", "set": "MXL"},
{"name": "NA19777", "set": "MXL"},
{"name": "NA19786", "set": "MXL"},
{"name": "NA19652", "set": "MXL"},
{"name": "NA19663", "set": "MXL"},
{"name": "NA19679", "set": "MXL"},
{"name": "NA19717", "set": "MXL"},
{"name": "NA19726", "set": "MXL"},
{"name": "NA19735", "set": "MXL"},
{"name": "NA19747", "set": "MXL"},
{"name": "NA19756", "set": "MXL"},
{"name": "NA19770", "set": "MXL"},
{"name": "NA19779", "set": "MXL"},
{"name": "NA19788", "set": "MXL"},
{"name": "NA19654", "set": "MXL"},
{"name": "NA19664", "set": "MXL"},
{"name": "NA19681", "set": "MXL"},
{"name": "NA19719", "set": "MXL"},
{"name": "NA19728", "set": "MXL"},
{"name": "NA19737", "set": "MXL"},
{"name": "NA19749", "set": "MXL"},
{"name": "NA19758", "set": "MXL"},
{"name": "NA19771", "set": "MXL"},
{"name": "NA19780", "set": "MXL"},
{"name": "NA19789", "set": "MXL"},
{"name": "NA19655", "set": "MXL"},
{"name": "NA19672", "set": "MXL"},
{"name": "NA19682", "set": "MXL"},
{"name": "NA19720", "set": "MXL"},
{"name": "NA19729", "set": "MXL"},
{"name": "NA19738", "set": "MXL"},
{"name": "NA19750", "set": "MXL"},
{"name": "NA19759", "set": "MXL"},
{"name": "NA19773", "set": "MXL"},
{"name": "NA19782", "set": "MXL"},
{"name": "NA19794", "set": "MXL"},
{"name": "NA19657", "set": "MXL"},
{"name": "NA19675", "set": "MXL"},
{"name": "NA19684", "set": "MXL"},
{"name": "NA19722", "set": "MXL"},
{"name": "NA19731", "set": "MXL"},
{"name": "NA19740", "set": "MXL"},
{"name": "NA19752", "set": "MXL"},
{"name": "NA19761", "set": "MXL"},
{"name": "NA19774", "set": "MXL"},
{"name": "NA19783", "set": "MXL"},
{"name": "NA19795", "set": "MXL"}
],
"chromosomes": [
{"name": "21", "length": 46944323, "display": "21 (47 Mbp)"},
{"name": "22", "length": 49691432, "display": "22 (50 Mbp)"}
],
"tracks": [
{
"name": "Integrated variants",
"description": "These represent an integrated variant call set based on both low coverage and exome sequencing data from 1092 individuals and contains snps, indels and larger deletions.",
"maximum_resolution": 1000000,
"files": {
"*": "ALL.chr<chrom>.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz"
},
"colors": {
"REF": [200,200,200,1],
"HET": [200,100,0,1],
"ALT": [200,0,0,1]
},
"type": "vcf"
},
{
"name": "Ancestry deconvolution",
"description": "Diploid ancestry calls are a consensus of calls that agree in >= 3 of 4 methods (LAMP-LD, HAPMIX, RFMIX and MULTIMIX) <br/> <br/> Dipoid ancestry tract code: <br/> 0 = unknown (a tie, 3-way or 4-way disagreement across methods) <br/> 1 = European:European <br/> 2 = European:African <br/> 3 = African:African <br/> 4 = European:Native American <br/> 5 = African:Native American <br/> 6 = Native American:Native American <br/> undet = base pairs between the SNP at the end of one tract and the first SNP at the beginning of the next tract. Regions at the start and end of each chromosome flanking the first and last SNPs used in the calling are also listed as 'undet'.",
"maximum_resolution": 0,
"files": {
"*": "<set>/<sample>.bed.gz"
},
"colors": {
"undet": [200,200,200,1],
"0": [0,0,0,1],
"1": [200,0,0,1],
"2": [0,200,0,1],
"3": [0,0,200,1],
"4": [200,200,0,1],
"5": [200,0,200,1],
"6": [0,200,200,1]
},
"type": "bed"
}
]
}