21 lines
2.4 KiB
Plaintext
21 lines
2.4 KiB
Plaintext
##fileformat=VCFv4.0
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##PhaseByTransmissionUnitTest="This file contains special cases for phasing by transmission such as missing genotypes. 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=NoCall_mother GT:GQ:PL ./.:.:. 0/0:40:0,40,200 0/1:30:30,0,200 ./.:.:. 0/1:30:30,0,200 ./.:.:.
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1 10147 . C A 99 PASS TestDescription=NoCall_father GT:GQ:PL 0/0:30:0,30,200 ./.:.:. 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=NoCall_child GT:GQ:PL 0/0:40:0,40,200 0/1:30:30,0,200 ./.:.:. 0/0:40:0,40,200 ./.:.:. 0/0:40:0,40,200
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1 10177 . A C 99 PASS TestDescription=Missing_mother GT:GQ:PL . 1/1:40:200,40,0 0/0:30:0,30,200 . 0/0:30:0,30,200 .
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1 10180 . T C 99 PASS TestDescription=Missing_father GT:GQ:PL 0/0:30:0,30,200 . 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 10234 . C T 99 PASS TestDescription=Missing_child GT:GQ:PL 0/1:40:40,0,200 0/0:30:0,30,200 . 0/1:40:40,0,200 . 0/1:40:40,0,200
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1 10235 . T A 99 PASS TestDescription=NoCall_parents GT:GQ:PL ./.:.:. ./.:.:. 0/0:30:0,30,200 ./.:.:. 0/0:30:0,30,200 ./.:.:.
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1 10236 . A G 99 PASS TestDescription=NoCall_all GT:GQ:PL ./.:.:. ./.:.:. ./.:.:. ./.:.:. ./.:.:. ./.:.:.
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1 10250 . A C 99 PASS TestDescription=Missing_parents GT:GQ:PL . . 1/1:50:200,50,0 . 1/1:50:200,50,0 .
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1 10257 . A C 99 PASS TestDescription=Missing_all GT:GQ:PL . . . . . .
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1 10285 . T C 99 PASS TestDescription=ZeroConfidence GT:GQ:PL 0/1:0:0,0,0 1/1:0:0,0,0 1/1:0:0,0,0 0/1:0:0,0,0 1/1:0:0,0,0 0/1:0:0,0,0
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1 10297 . C T 99 PASS TestDescription=ZeroConfidenceParents GT:GQ:PL 1/1:0:0,0,0 0/0:0:0,0,0 0/1:10:10,0,50 1/1:0:0,0,0 0/1:10:10,0,50 1/1:0:0,0,0
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1 10304 . A C 99 PASS TestDescription=ZeroConfidenceChild GT:GQ:PL 1/1:50:200,50,0 0/1:50:50,0,200 0/1:0:0,0,0 1/1:50:200,50,0 0/1:0:0,0,0 1/1:50:200,50,0
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