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genome.toml
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genome.toml
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name = 'hg38'
chromsize =[
248956422,
242193529,
198295559,
190214555,
181538259,
170805979,
159345973,
145138636,
138394717,
133797422,
135086622,
133275309,
114364328,
107043718,
101991189,
90338345,
83257441,
80373285,
58617616,
64444167,
46709983,
50818468,
]
# formal names
chromnames = [
"chr1",
"chr2",
"chr3",
"chr4",
"chr5",
"chr6",
"chr7",
"chr8",
"chr9",
"chr10",
"chr11",
"chr12",
"chr13",
"chr14",
"chr15",
"chr16",
"chr17",
"chr18",
"chr19",
"chr20",
"chr21",
"chr22",
]
gmaps =[
"testdata/plink.GRCh38.map/plink.chr1.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr2.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr3.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr4.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr5.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr6.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr7.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr8.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr9.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr10.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr11.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr12.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr13.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr14.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr15.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr16.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr17.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr18.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr19.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr20.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr21.GRCh38.map",
"testdata/plink.GRCh38.map/plink.chr22.GRCh38.map",
]
# The index values must start from 0 and then increment by 1
[idx]
chr1 = 0
chr2 = 1
chr3 = 2
chr4 = 3
chr5 = 4
chr6 = 5
chr7 = 6
chr8 = 7
chr9 = 8
chr10 = 9
chr11 = 10
chr12 = 11
chr13 = 12
chr14 = 13
chr15 = 14
chr16 = 15
chr17 = 16
chr18 = 17
chr19 = 18
chr20 = 19
chr21 = 20
chr22 = 21
# allow alterative chromosome names map to mapped to the correct index
"1" = 0
"2" = 1
"3" = 2
"4" = 3
"5" = 4
"6" = 5
"7" = 6
"8" = 7
"9" = 8
"10" = 9
"11" = 10
"12" = 11
"13" = 12
"14" = 13
"15" = 14
"16" = 15
"17" = 16
"18" = 17
"19" = 18
"20" = 19
"21" = 20
"22" = 21