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- tests INFO:CN can be float - tests multiple symbolic alleles/SVLEN/SVCLAIM - tests SVCLAIM DJ type - Test Copy number as genotypes failed_CNV_001.vcf - Test SVCLAIM Is not D, J or DJ failed_CNV_002.vcf - Number of SVCLAIM failed_CNV_003.vcf - SVCLAIM is missing for a DEL symbolic allele
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=SVCLAIM Is not D, J or DJ | ||
| ##ALT=<ID=CNV,Description="Copy number variable region"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record"> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively"> | ||
| ##contig=<ID=1,length=1000000> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 1100 . C <CNV> 100 PASS CN=1.97;END=1200;SVLEN=100;SVCLAIM=JD GT 0|1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=Only one SVCLAIM where there should be two | ||
| ##ALT=<ID=CNV,Description="Copy number variable region"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record"> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively"> | ||
| ##contig=<ID=1,length=1000000> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 1100 . T <CNV>,<CNV> 100 PASS CN=2,4;END=1300;SVLEN=100,50;SVCLAIM=D GT 1|2 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=SVCLAIM is missing for a DEL symbolic allele | ||
| ##ALT=<ID=CNV,Description="Copy number variable region"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record"> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##contig=<ID=1,length=1000000> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 1100 . T <DEL> 100 PASS CN=0;END=1200;SVLEN=100 GT 0/1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,15 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##ALT=<ID=CNV,Description="Copy number variable region"> | ||
| ##INFO=<ID=MATEID,Number=A,Type=String,Description="ID of mate breakend"> | ||
| ##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the longest variant described in this record"> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ for abundance, adjacency and both respectively"> | ||
| ##contig=<ID=1,length=1000000> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 HG00097 | ||
| 1 1100 . C <DUP> 100 PASS CN=1.97;END=1200;SVLEN=100;SVCLAIM=D GT 0|1 0|0 | ||
| 1 1200 . T <DUP>,<DUP> 100 PASS CN=2,4;END=1300;SVLEN=100,50;SVCLAIM=D,D GT 1|2 0|1 | ||
| 1 1300 . C <DUP:TANDEM> 100 PASS CN=2;END=1310;SVLEN=10;SVCLAIM=DJ GT 1|0 0|0 | ||
| 1 1400 . C <CNV> 100 PASS END=1500;SVLEN=100 GT:CN .|.:3 .|.:2.1 |