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Fixes GenotypeConcordance VCF context with different Ref alleles or s…
…ymbolic allele
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,43 @@ | ||
##fileformat=VCFv4.1 | ||
##FILTER=<ID=Uncertain,Description="Uncertain genotype due to reason in filter INFO field"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, defined as difference between most likely and next most likely genotype likelihoods"> | ||
##FORMAT=<ID=GT,Number=1,Type=String,Description="Net Genotype across all datasets"> | ||
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants"> | ||
##contig=<ID=1,length=249250621> | ||
##contig=<ID=2,length=243199373> | ||
##contig=<ID=3,length=198022430> | ||
##contig=<ID=4,length=191154276> | ||
##contig=<ID=5,length=180915260> | ||
##contig=<ID=6,length=171115067> | ||
##contig=<ID=7,length=159138663> | ||
##contig=<ID=8,length=146364022> | ||
##contig=<ID=9,length=141213431> | ||
##contig=<ID=10,length=135534747> | ||
##contig=<ID=11,length=135006516> | ||
##contig=<ID=12,length=133851895> | ||
##contig=<ID=13,length=115169878> | ||
##contig=<ID=14,length=107349540> | ||
##contig=<ID=15,length=102531392> | ||
##contig=<ID=16,length=90354753> | ||
##contig=<ID=17,length=81195210> | ||
##contig=<ID=18,length=78077248> | ||
##contig=<ID=19,length=59128983> | ||
##contig=<ID=20,length=63025520> | ||
##contig=<ID=21,length=48129895> | ||
##contig=<ID=22,length=51304566> | ||
##contig=<ID=X,length=155270560> | ||
##contig=<ID=Y,length=59373566> | ||
##contig=<ID=MT,length=16569> | ||
##fileDate=20130719 | ||
##phasing=none | ||
##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta | ||
##source=SelectVariants | ||
##variants_justified=left | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT truth | ||
1 1 . TCAAGGG TGGG 22132 PASS set=Intersection GT:GQ 0/1:99 | ||
1 10 . TCAACAA TCAA 22132 PASS set=Intersection GT:GQ 0/1:99 | ||
1 100 . TCAACAA TCAACAAGG 10461 PASS set=Intersection GT:GQ 0/1:99 | ||
1 1000 . TCAACAA T 10461 PASS set=Intersection GT:GQ ./. | ||
1 1100 . TCAACAA T 10461 PASS set=Intersection GT:GQ 0/1:99 | ||
1 1200 . TCAACAA T 10461 PASS set=Intersection GT:GQ ./. | ||
1 1300 . TCAACAA <ID> 10461 PASS set=Intersection GT:GQ 0/1:99 |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,42 @@ | ||
##fileformat=VCFv4.1 | ||
##FILTER=<ID=Uncertain,Description="Uncertain genotype due to reason in filter INFO field"> | ||
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Net Genotype quality across all datasets, defined as difference between most likely and next most likely genotype likelihoods"> | ||
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants"> | ||
##contig=<ID=1,length=249250621> | ||
##contig=<ID=2,length=243199373> | ||
##contig=<ID=3,length=198022430> | ||
##contig=<ID=4,length=191154276> | ||
##contig=<ID=5,length=180915260> | ||
##contig=<ID=6,length=171115067> | ||
##contig=<ID=7,length=159138663> | ||
##contig=<ID=8,length=146364022> | ||
##contig=<ID=9,length=141213431> | ||
##contig=<ID=10,length=135534747> | ||
##contig=<ID=11,length=135006516> | ||
##contig=<ID=12,length=133851895> | ||
##contig=<ID=13,length=115169878> | ||
##contig=<ID=14,length=107349540> | ||
##contig=<ID=15,length=102531392> | ||
##contig=<ID=16,length=90354753> | ||
##contig=<ID=17,length=81195210> | ||
##contig=<ID=18,length=78077248> | ||
##contig=<ID=19,length=59128983> | ||
##contig=<ID=20,length=63025520> | ||
##contig=<ID=21,length=48129895> | ||
##contig=<ID=22,length=51304566> | ||
##contig=<ID=X,length=155270560> | ||
##contig=<ID=Y,length=59373566> | ||
##contig=<ID=MT,length=16569> | ||
##fileDate=20130719 | ||
##phasing=none | ||
##reference=file:///seq/references/Homo_sapiens_assembly19/v1/Homo_sapiens_assembly19.fasta | ||
##source=SelectVariants | ||
##variants_justified=left | ||
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT truth | ||
1 1 . TCAA T 22132 PASS set=Intersection GT:GQ 0/1:99 | ||
1 10 . TCAA T 22132 PASS set=Intersection GT:GQ 0/1:99 | ||
1 100 . TCAA TCAAGG 10461 PASS set=Intersection GT:GQ 0/1:99 | ||
1 1000 . TCAA T 10461 PASS set=Intersection GT:GQ ./. | ||
1 1100 . TCAA T 10461 PASS set=Intersection GT:GQ ./. | ||
1 1200 . TCAA T 10461 PASS set=Intersection GT:GQ 0/1:99 | ||
1 1300 . TCAA <ID> 10461 PASS set=Intersection GT:GQ 0/1:99 |