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25
test/input_files/v4.4/failed/failed_body_invalid_CNVTR_1.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid info field on CNV:TR RN-RUS-RUL | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 70 rs180734498 C <CNV:TR> 100 PASS SVLEN=10 GT 0|0 | ||
| 1 80 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=2;RUL=3 GT 0|0 | ||
| 1 90 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TG,TA GT 0|0 | ||
| 1 90 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=2;RUL=2 GT 0|0 | ||
| 1 100 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=1;RUS=T,A GT 0|0 | ||
| 1 110 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=1;RUL=2;RUS=T,A GT 0|0 | ||
| 1 120 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=1;RUL=2;RUS=. GT 0|0 |
39 changes: 39 additions & 0 deletions
39
test/input_files/v4.4/failed/failed_body_invalid_CNVTR_2.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid info field on CNV:TR RN - RUC, RB, CIRUC, CIRB | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##INFO=<ID=CIRUC,Number=.,Type=Float,Description="Confidence interval around RUC"> | ||
| ##INFO=<ID=CIRB,Number=.,Type=Integer,Description="Confidence interval around RB"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 70 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TT;RUC=2,2 GT 0|0 | ||
| 1 80 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=2;RUL=2,10;RUC=3 GT 0|0 | ||
| 1 90 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=2;RUL=2,10;RB=3 GT 0|0 | ||
| 1 100 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=1 GT 0|0 | ||
| 1 110 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=1,. GT 0|0 | ||
| 1 120 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=.,-1 GT 0|0 | ||
| 1 130 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=1,-1 GT 0|0 | ||
| 1 140 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=-1,-1 GT 0|0 | ||
| 1 150 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RB=30;CIRB=-8,8,9 GT 0|0 | ||
| 1 160 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT,TT;RB=.,20;CIRB=-8,8,-9,0 GT 0|0 | ||
| 1 170 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT,TT;CIRB=-8,8 GT 0|0 | ||
| 1 200 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3.2;CIRUC=1 GT 0|0 | ||
| 1 210 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3.2;CIRUC=1,. GT 0|0 | ||
| 1 220 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3.2;CIRUC=.,-1 GT 0|0 | ||
| 1 230 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3.2;CIRUC=1,-1 GT 0|0 | ||
| 1 240 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3.2;CIRUC=-1,-1 GT 0|0 | ||
| 1 250 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT;RUC=3;CIRUC=-8,8,9 GT 0|0 | ||
| 1 260 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT,TT;RUC=.,2;CIRUC=-8,8,-9,0 GT 0|0 | ||
| 1 270 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=AT,TT;CIRUC=-8,8,-9,0 GT 0|0 |
23 changes: 23 additions & 0 deletions
23
test/input_files/v4.4/failed/failed_body_invalid_CNVTR_3.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,23 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid info field on CNV:TR RN - RUC, RB; warning: RB ~= RUC * RUL; error to make this fail: RUC not integer with RUB | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##INFO=<ID=CIRUC,Number=.,Type=Float,Description="Confidence interval around RUC"> | ||
| ##INFO=<ID=CIRB,Number=.,Type=Integer,Description="Confidence interval around RB"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 70 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TT;RUC=2.3;RB=5 GT 0|0 | ||
| 1 80 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUL=2;RUC=2.3;RB=5 GT 0|0 | ||
| 1 90 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUL=2;RUC=2.3;RB=5;RUB=10 GT 0|0 |
24 changes: 24 additions & 0 deletions
24
test/input_files/v4.4/failed/failed_body_invalid_CNVTR_4.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,24 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid info field on CNV:TR RN - RUB, RUC | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##INFO=<ID=CIRUC,Number=.,Type=Float,Description="Confidence interval around RUC"> | ||
| ##INFO=<ID=CIRB,Number=.,Type=Integer,Description="Confidence interval around RB"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 70 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TT;RUC=2.3;RUB=2 GT 0|0 | ||
| 1 80 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RN=2;RUS=TT,AA;RUC=.,2;RUB=2,2 GT 0|0 | ||
| 1 90 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TT;RUC=2;RUB=2 GT 0|0 | ||
| 1 100 rs180734498 C <CNV:TR> 100 PASS SVLEN=10;RUS=TT;RUB=2 GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##ALT=<ID=DEL,Description="Deletion"> | ||
| ##ALT=<ID=INS> | ||
| ##FILTER=<ID=F1,Description="Filter1"> | ||
| ##FILTER=<ID=F2> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <DAL:TRE> 100 PASS SVLEN=1;SVCLAIM=D GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV - SVLEN not present | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##ALT=<ID=DEL,Description="Deletion"> | ||
| ##ALT=<ID=INS> | ||
| ##FILTER=<ID=F1,Description="Filter1"> | ||
| ##FILTER=<ID=F2> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <DEL> 100 PASS SVCLAIM=D GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV - SVCLAIM not present for DEL/DUP | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##ALT=<ID=DEL,Description="Deletion"> | ||
| ##ALT=<ID=DUP,Description="Duplication"> | ||
| ##ALT=<ID=INV,Description="Inversion"> | ||
| ##ALT=<ID=INS> | ||
| ##FILTER=<ID=F1,Description="Filter1"> | ||
| ##FILTER=<ID=F2> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <INV> 100 PASS SVLEN=10 GT 0|0 | ||
| 1 700 rs180734498 C <DEL> 100 PASS SVLEN=10 GT 0|0 | ||
| 1 700 rs180734498 C <DUP> 100 PASS SVLEN=10 GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV - CNV:TR must have RUS/RUL | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUS=TTT GT 0|0 | ||
| 1 800 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUL=3 GT 0|0 | ||
| 1 900 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV - CNV:TR - RB ~= RUL * RUC | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUS=TTT;RUC=30;RB=100 GT 0|0 | ||
| 1 800 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUL=3;RUC=30;RB=100 GT 0|0 | ||
| 1 900 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUS=TTT;RUL=2 GT 0|0 | ||
| 1 1000 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUS=TTT;RUL=3 GT 0|0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid SV - BND | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##ALT=<ID=BND:Test,Description="Breakend SV acceptable in v4.3"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <BND:Test> 100 PASS CN=100;SVLEN=1 GT 0|0 | ||
|
|
21 changes: 21 additions & 0 deletions
21
test/input_files/v4.4/failed/failed_body_invalid_format_1.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,21 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid format fields, with CICN, format CN must be present | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##INFO=<ID=RN,Number=A,Type=Integer,Description="Total number of repeat sequences in this allele"> | ||
| ##INFO=<ID=RUS,Number=.,Type=String,Description="Repeat unit sequence of the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUC,Number=.,Type=Float,Description="Repeat unit count of corresponding repeat sequence"> | ||
| ##INFO=<ID=RB,Number=.,Type=Integer,Description="Total number of bases in the corresponding repeat sequence"> | ||
| ##INFO=<ID=RUB,Number=.,Type=Integer,Description="Number of bases in each individual repeat unit"> | ||
| ##INFO=<ID=RUL,Number=.,Type=Integer,Description="Repeat unit length of the corresponding repeat sequence"> | ||
| ##ALT=<ID=CNV:TR,Description="Tandem repeat determined based on DNA abundance"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUS=TTT GT:CN 0|0:2 | ||
| 1 800 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUL=3 GT:CN:CICN 0|0:2:-1,1 | ||
| 1 900 rs180734498 C <CNV:TR> 100 PASS CN=100;SVLEN=1;SVCLAIM=D;RUL=3 GT:CICN 0|0:-1,2 |
17 changes: 17 additions & 0 deletions
17
test/input_files/v4.4/failed/failed_body_invalid_format_2.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid format fields, SVLEN must be same for DEL/DUP/CNV when format CN is present | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##ALT=<ID=CNV,Description="CNV"> | ||
| ##ALT=<ID=DEL,Description="DEL"> | ||
| ##ALT=<ID=DUP,Description="DUP"> | ||
| ##FORMAT=<ID=CN,Number=1,Type=Float,Description="Copy number"> | ||
| ##FORMAT=<ID=CICN,Number=2,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 700 rs180734498 C <DEL>,T,<DUP> 100 PASS SVLEN=1,.,2;SVCLAIM=D,.,D GT:CN 0|0:2 | ||
| 1 800 rs180734498 C <CNV>,T,<DEL> 100 PASS SVLEN=2,.,1;SVCLAIM=D,.,DJ GT:CN:CICN 0|0:2:-1,1 | ||
| 1 900 rs180734498 C <CNV>,T,<DUP> 100 PASS SVLEN=1,.,21;SVCLAIM=D,.,J GT:CN:CICN 0|0:2:-1,2 |
17 changes: 17 additions & 0 deletions
17
test/input_files/v4.4/failed/failed_body_invalid_info_CICN.vcf
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,17 @@ | ||
| ##fileformat=VCFv4.4 | ||
| ##CauseOfFailure=invalid info CICN value | ||
| ##reference=testval | ||
| ##contig=<ID=1,length=6243,assembly=B3,md5=f121111111618ff66beb2da,species="Homo sapiens",taxonomy=x> | ||
| ##INFO=<ID=SVCLAIM,Number=A,Type=String,Description="Claim made by the structural variant call. Valid values are D, J, DJ..."> | ||
| ##INFO=<ID=SVLEN,Number=A,Type=Integer,Description="Length of structural variant"> | ||
| ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | ||
| ##INFO=<ID=CN,Number=A,Type=Float,Description="Copy number of CNV/breakpoint"> | ||
| ##ALT=<ID=CNV,Description="CNV"> | ||
| ##INFO=<ID=CICN,Number=.,Type=Float,Description="Confidence interval around copy number"> | ||
| #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00096 | ||
| 1 800 rs180734498 C <CNV> 100 PASS SVLEN=2;SVCLAIM=D;CN=1.2;CICN=-1 GT 0/0 | ||
| 1 900 rs180734498 C <CNV> 100 PASS SVLEN=1;SVCLAIM=D;CN=1.2;CICN=-2,-1 GT 0/0 | ||
| 1 1000 rs180734498 C <CNV> 100 PASS SVLEN=1;SVCLAIM=D;CN=1.2;CICN=1,1.1 GT 0/0 | ||
| 1 1100 rs180734498 C <CNV> 100 PASS SVLEN=1;SVCLAIM=D;CN=1.2;CICN=-1.5,1.4 GT 0/0 | ||
| 1 1200 rs180734498 C <CNV> 100 PASS SVLEN=1;SVCLAIM=D;CN=1.2;CICN=1,5 GT 0/0 | ||
| 1 1300 rs180734498 C <CNV> 100 PASS SVLEN=1;SVCLAIM=D GT:CN:CICN 0/0:1.2:1,1,1 |
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