Skip to content

HTTPS clone URL

Subversion checkout URL

You can clone with
or
.
Download ZIP
Browse files

Test data for testing the fix for issue #140

  • Loading branch information...
commit d51db2303913b725612a29ad07b34968e947cfa3 1 parent ce4d20f
datagram authored casbon committed
View
35 vcf/test/issue-140-file1.vcf
@@ -0,0 +1,35 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL
+chr1 10 . G GGT . PASS DP=91;SS=1;SSC=2;GPV=3.0109E-23;SPV=5.8324E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:13:22:62.86%:2,11,1,21
+chr1 20 . GT G . PASS DP=77;SS=1;SSC=2;GPV=2.4504E-29;SPV=6.0772E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:28:5:22:81.48%:0,5,1,21
+chr2 30 . AC A . PASS DP=22;SS=1;SSC=7;GPV=1.3117E-10;SPV=1.9481E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:10:2:8:80%:0,2,0,8
+chr2 40 . AAAC A . PASS DP=42;SS=1;SSC=12;GPV=7.3092E-18;SPV=6.278E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:4:9:69.23%:4,0,9,0
+chr3 50 . TC T . PASS DP=41;SS=1;SSC=2;GPV=9.8874E-23;SPV=5.3659E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:22:1:21:95.45%:1,0,15,6
+chr10 60 . T TTAA . PASS DP=27;SS=1;SSC=2;GPV=1.4382E-14;SPV=5.5556E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:12:0:12:100%:0,0,0,12
+chr10 70 . C CTG . PASS DP=40;SS=1;SSC=7;GPV=3.6006E-9;SPV=1.9922E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:10:6:4:40%:0,6,0,4
+chr11 80 . AGTT A . PASS DP=86;SS=1;SSC=0;GPV=4.1554E-34;SPV=8.5795E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:32:4:28:87.5%:1,3,0,28
+chr11 90 . GA G . PASS DP=41;SS=1;SSC=3;GPV=1.9197E-12;SPV=4.089E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:15:5:9:64.29%:1,4,0,9
+chr20 100 . TTTTG T . PASS DP=23;SS=1;SSC=1;GPV=2.9149E-12;SPV=6.5217E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:8:0:8:100%:0,0,7,1
+chr20 110 . GA G . PASS DP=83;SS=1;SSC=13;GPV=1E0;SPV=4.0806E-2 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:35:5:28:84.85%:4,1,12,16
+chrX 120 . G GA . PASS DP=61;SS=1;SSC=1;GPV=1.6967E-25;SPV=7.0485E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:22:3:19:86.36%:0,3,1,18
+chrX 130 . T TAA . PASS DP=19;SS=1;SSC=1;GPV=1.1285E-5;SPV=7.2172E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:8:2:5:71.43%:0,2,0,5
+chrY 140 . G GTTT . PASS DP=62;SS=1;SSC=0;GPV=3.4914E-15;SPV=9.571E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:2:19:90.48%:1,1,15,4
+chrY 150 . T TGAAG . PASS DP=28;SS=1;SSC=12;GPV=1.7583E-10;SPV=5.5797E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:5:8:61.54%:4,1,2,6
+chrM 160 . G GTTT . PASS DP=62;SS=1;SSC=0;GPV=3.4914E-15;SPV=9.571E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:2:19:90.48%:1,1,15,4
+chrM 170 . T TGAAG . PASS DP=28;SS=1;SSC=12;GPV=1.7583E-10;SPV=5.5797E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:5:8:61.54%:4,1,2,6
View
34 vcf/test/issue-140-file2.vcf
@@ -0,0 +1,34 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL
+chr1 10 . G GGT . PASS DP=91;SS=1;SSC=2;GPV=3.0109E-23;SPV=5.8324E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:13:22:62.86%:2,11,1,21
+chr1 20 . GT G . PASS DP=77;SS=1;SSC=2;GPV=2.4504E-29;SPV=6.0772E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:28:5:22:81.48%:0,5,1,21
+chr2 30 . AC A . PASS DP=22;SS=1;SSC=7;GPV=1.3117E-10;SPV=1.9481E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:10:2:8:80%:0,2,0,8
+chr2 41 . AAAC A . PASS DP=42;SS=1;SSC=12;GPV=7.3092E-18;SPV=6.278E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:4:9:69.23%:4,0,9,0
+chr10 60 . T TTAA . PASS DP=27;SS=1;SSC=2;GPV=1.4382E-14;SPV=5.5556E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:12:0:12:100%:0,0,0,12
+chr10 70 . C CTG . PASS DP=40;SS=1;SSC=7;GPV=3.6006E-9;SPV=1.9922E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:10:6:4:40%:0,6,0,4
+chr11 80 . AGTT A . PASS DP=86;SS=1;SSC=0;GPV=4.1554E-34;SPV=8.5795E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:32:4:28:87.5%:1,3,0,28
+chr11 91 . GA G . PASS DP=41;SS=1;SSC=3;GPV=1.9197E-12;SPV=4.089E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:15:5:9:64.29%:1,4,0,9
+chr20 100 . TTTTG T . PASS DP=23;SS=1;SSC=1;GPV=2.9149E-12;SPV=6.5217E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:8:0:8:100%:0,0,7,1
+chr20 110 . GA G . PASS DP=83;SS=1;SSC=13;GPV=1E0;SPV=4.0806E-2 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:35:5:28:84.85%:4,1,12,16
+chrX 120 . G GA . PASS DP=61;SS=1;SSC=1;GPV=1.6967E-25;SPV=7.0485E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:22:3:19:86.36%:0,3,1,18
+chrX 130 . T TAA . PASS DP=19;SS=1;SSC=1;GPV=1.1285E-5;SPV=7.2172E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:8:2:5:71.43%:0,2,0,5
+chrY 140 . G GTTT . PASS DP=62;SS=1;SSC=0;GPV=3.4914E-15;SPV=9.571E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:2:19:90.48%:1,1,15,4
+chrY 149 . T TGAAG . PASS DP=28;SS=1;SSC=12;GPV=1.7583E-10;SPV=5.5797E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:5:8:61.54%:4,1,2,6
+chrM 160 . G GTTT . PASS DP=62;SS=1;SSC=0;GPV=3.4914E-15;SPV=9.571E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:36:2:19:90.48%:1,1,15,4
+chrM 170 . T TGAAG . PASS DP=28;SS=1;SSC=12;GPV=1.7583E-10;SPV=5.5797E-2 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:13:5:8:61.54%:4,1,2,6
View
25 vcf/test/issue-140-file3.vcf
@@ -0,0 +1,25 @@
+##fileformat=VCFv4.1
+##source=VarScan2
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total depth of quality bases">
+##INFO=<ID=SOMATIC,Number=0,Type=Flag,Description="Indicates if record is a somatic mutation">
+##INFO=<ID=SS,Number=1,Type=String,Description="Somatic status of variant (0=Reference,1=Germline,2=Somatic,3=LOH, or 5=Unknown)">
+##INFO=<ID=SSC,Number=1,Type=String,Description="Somatic score in Phred scale (0-255) derived from somatic p-value">
+##INFO=<ID=GPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor+normal versus no variant for Germline calls">
+##INFO=<ID=SPV,Number=1,Type=Float,Description="Fisher's Exact Test P-value of tumor versus normal for Somatic/LOH calls">
+##FILTER=<ID=str10,Description="Less than 10% or more than 90% of variant supporting reads on one strand">
+##FILTER=<ID=indelError,Description="Likely artifact due to indel reads at this position">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=RD,Number=1,Type=Integer,Description="Depth of reference-supporting bases (reads1)">
+##FORMAT=<ID=AD,Number=1,Type=Integer,Description="Depth of variant-supporting bases (reads2)">
+##FORMAT=<ID=FREQ,Number=1,Type=String,Description="Variant allele frequency">
+##FORMAT=<ID=DP4,Number=1,Type=String,Description="Strand read counts: ref/fwd, ref/rev, var/fwd, var/rev">
+#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NORMAL
+chr3 50 . TC T . PASS DP=41;SS=1;SSC=2;GPV=9.8874E-23;SPV=5.3659E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:22:1:21:95.45%:1,0,15,6
+chr10 60 . T TTAA . PASS DP=27;SS=1;SSC=2;GPV=1.4382E-14;SPV=5.5556E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:12:0:12:100%:0,0,0,12
+chr10 70 . C CTG . PASS DP=40;SS=1;SSC=7;GPV=3.6006E-9;SPV=1.9922E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:10:6:4:40%:0,6,0,4
+chr11 80 . AGTT A . PASS DP=86;SS=1;SSC=0;GPV=4.1554E-34;SPV=8.5795E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:32:4:28:87.5%:1,3,0,28
+chr11 90 . GA G . PASS DP=41;SS=1;SSC=3;GPV=1.9197E-12;SPV=4.089E-1 GT:GQ:DP:RD:AD:FREQ:DP4 0/1:.:15:5:9:64.29%:1,4,0,9
+chr20 100 . TTTTG T . PASS DP=23;SS=1;SSC=1;GPV=2.9149E-12;SPV=6.5217E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:8:0:8:100%:0,0,7,1
+chrX 120 . G GA . PASS DP=61;SS=1;SSC=1;GPV=1.6967E-25;SPV=7.0485E-1 GT:GQ:DP:RD:AD:FREQ:DP4 1/1:.:22:3:19:86.36%:0,3,1,18
Please sign in to comment.
Something went wrong with that request. Please try again.