20 lines
2.9 KiB
Plaintext
20 lines
2.9 KiB
Plaintext
##fileformat=VCFv4.0
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##PhaseByTransmissionUnitTest="This file contains only genotypes with false mendelian violations in the input data. The output data should correct the genotypes and phase the trios. The pair should be corrected and phased where possible. Genotype combination phred score should be reported where possible. The unrelated individual should remain untouched. Please note that this file is entirely synthetic and does not represent true SNPs or genotypes observed."
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##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
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##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
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##FORMAT=<ID=PL,Number=3,Type=Float,Description="Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic">
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##INFO=<ID=TestDescription,Number=1,Type=String,Description="Test case evaluated at this locus.">
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#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT TRIO_MOTHER TRIO_FATHER TRIO_CHILD PAIR_FATHER PAIR_CHILD UNRELATED_INDIVIDUAL_CONTROL
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1 10109 . A T 99 PASS TestDescription=HomRef/HomRef/Het GT:GQ:PL 0/0:50:0,50,200 0/0:40:0,40,200 0/1:30:30,0,200 0/0:50:0,50,200 0/1:30:30,0,200 0/0:50:0,50,200
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1 10147 . C A 99 PASS TestDescription=HomRef/HomRef/HomAlt GT:GQ:PL 0/0:30:0,30,200 0/0:50:0,50,200 1/1:40:200,40,0 0/0:30:0,30,200 1/1:40:200,40,0 0/0:30:0,30,200
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1 10150 . C T 99 PASS TestDescription=HomRef/Het/HomAlt GT:GQ:PL 0/0:40:0,40,200 0/1:30:30,0,200 1/1:50:200,50,0 0/0:40:0,40,200 1/1:50:200,50,0 0/0:40:0,40,200
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1 10177 . A C 99 PASS TestDescription=HomRef/HomAlt/HomRef GT:GQ:PL 0/0:50:0,50,200 1/1:40:200,40,0 0/0:30:0,30,200 0/0:50:0,50,200 0/0:30:0,30,200 0/0:50:0,50,200
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1 10180 . T C 99 PASS TestDescription=HomRef/HomAlt/HomAlt GT:GQ:PL 0/0:30:0,30,200 1/1:50:200,50,0 1/1:40:200,40,0 0/0:30:0,30,200 1/1:40:200,40,0 0/0:30:0,30,200
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1 10234 . C T 99 PASS TestDescription=Het/HomRef/HomAlt GT:GQ:PL 0/1:40:40,0,200 0/0:30:0,30,200 1/1:50:200,50,0 0/1:40:40,0,200 1/1:50:200,50,0 0/1:40:40,0,200
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1 10235 . T A 99 PASS TestDescription=Het/HomAlt/HomRef GT:GQ:PL 0/1:50:50,0,200 1/1:40:200,40,0 0/0:30:0,30,200 0/1:50:50,0,200 0/0:30:0,30,200 0/1:50:50,0,200
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1 10236 . A G 99 PASS TestDescription=HomVar/HomRef/HomRef GT:GQ:PL 1/1:30:200,30,0 0/0:50:0,50,200 0/0:40:0,40,200 1/1:30:200,30,0 0/0:50:0,50,200 1/1:30:200,30,0
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1 10250 . A C 99 PASS TestDescription=HomVar/HomRef/HomVar GT:GQ:PL 1/1:40:200,40,0 0/0:30:0,30,200 1/1:50:200,50,0 1/1:40:200,40,0 1/1:50:200,50,0 1/1:40:200,40,0
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1 10257 . A C 99 PASS TestDescription=HomVar/Het/HomRef GT:GQ:PL 1/1:50:200,50,0 0/1:40:40,0,200 0/0:30:0,30,200 1/1:50:200,50,0 0/0:30:0,30,200 1/1:50:200,50,0
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1 10285 . T C 99 PASS TestDescription=HomVar/HomVar/Het GT:GQ:PL 1/1:30:200,30,0 1/1:50:200,50,0 0/1:40:40,0,200 1/1:30:200,30,0 0/1:40:40,0,200 1/1:30:200,30,0
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1 10297 . C T 99 PASS TestDescription=HomVar/HomVar/HomRef GT:GQ:PL 1/1:40:200,40,0 1/1:30:200,30,0 0/0:50:0,50,200 1/1:40:200,40,0 0/0:50:0,50,200 1/1:40:200,40,0
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