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Searched refs:GT (Results 51 – 75 of 12460) sorted by relevance

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/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/GenomicsDBImport/
H A D	expected.testGenomicsDBImportWithNonDiploidData.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 205 20 10001427 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:53:5:53:0,5,1899 ./. 209 20 10001433 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:56:0:56:0,0,1779 ./. 211 20 10001435 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:55:0:55:0,0,1790 ./. 238 20 10002457 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:52:0:52:0,0,1572 ./. 250 20 10002482 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:46:3:46:0,3,1461 ./. 591 20 10012549 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:6:1:6:0,1,186 ./. 743 20 10015599 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:3:9:3:0,9,109 ./. 1490 20 10098344 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:4:0:4:0,0,1 ./. 1505 20 10098713 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL ./.:8:0:8:0,0,262 ./. [all …]
H A D	expected.testGVCFMode.gatk4.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 112 20 10001427 . T <NON_REF> . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899 114 20 10001430 . G <NON_REF> . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743 156 20 10002478 . A <NON_REF> . . END=10002481 GT:DP:GQ:MIN_DP:PL 0/0:56:0:50:0,0,731 614 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0 615 20 10015566 . G <NON_REF> . . END=10015580 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45 616 20 10015581 . G <NON_REF> . . END=10015598 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69 1231 20 10098344 . A <NON_REF> . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1 1234 20 10098361 . T <NON_REF> . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 1236 20 10098455 . A <NON_REF> . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/haplotypecaller/
H A D	expected.testGVCFMode.3.8-4-g7b0250253f.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 135 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0 269 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 288 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0 302 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0 322 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 342 20 10008950 . A <NON_REF> . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0 588 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90 589 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45 590 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0 [all …]
H A D	expected.testGVCFMode.gatk4.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 111 20 10001427 . T <NON_REF> . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899 113 20 10001430 . G <NON_REF> . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743 155 20 10002478 . A <NON_REF> . . END=10002481 GT:DP:GQ:MIN_DP:PL 0/0:56:0:50:0,0,731 614 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0 615 20 10015566 . G <NON_REF> . . END=10015580 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45 616 20 10015581 . G <NON_REF> . . END=10015598 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69 1231 20 10098344 . A <NON_REF> . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1 1234 20 10098361 . T <NON_REF> . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 1236 20 10098455 . A <NON_REF> . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 [all …]
H A D	expected.testGVCFMode.gatk3.5.alleleSpecific.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 142 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0 276 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 295 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0 309 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0 329 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 597 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90 598 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45 599 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0 741 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0 [all …]
H A D	expected.testGVCFMode.gatk3.8-4-g7b0250253f.alleleSpecific.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 142 20 10001437 . A <NON_REF> . . END=10001437 GT:DP:GQ:MIN_DP:PL 0/0:57:0:57:0,0,0 276 20 10006824 . A <NON_REF> . . END=10006824 GT:DP:GQ:MIN_DP:PL 0/0:75:0:75:0,0,0 295 20 10008030 . A <NON_REF> . . END=10008030 GT:DP:GQ:MIN_DP:PL 0/0:91:0:91:0,0,0 309 20 10008148 . A <NON_REF> . . END=10008148 GT:DP:GQ:MIN_DP:PL 0/0:74:0:74:0,0,0 329 20 10008759 . A <NON_REF> . . END=10008759 GT:DP:GQ:MIN_DP:PL 0/0:55:0:55:0,0,0 349 20 10008950 . A <NON_REF> . . END=10008951 GT:DP:GQ:MIN_DP:PL 0/0:48:0:48:0,0,0 595 20 10012556 . T <NON_REF> . . END=10012557 GT:DP:GQ:MIN_DP:PL 0/0:9:6:9:0,6,90 596 20 10012558 . C <NON_REF> . . END=10012558 GT:DP:GQ:MIN_DP:PL 0/0:9:3:9:0,3,45 597 20 10012559 . C <NON_REF> . . END=10012569 GT:DP:GQ:MIN_DP:PL 0/0:9:0:8:0,0,0 [all …]
H A D	expected.testGVCFMode.gatk4.alleleSpecific.g.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 118 20 10001427 . T <NON_REF> . . END=10001427 GT:DP:GQ:MIN_DP:PL 0/0:53:5:53:0,5,1899 120 20 10001430 . G <NON_REF> . . END=10001431 GT:DP:GQ:MIN_DP:PL 0/0:56:0:56:0,0,1743 162 20 10002478 . A <NON_REF> . . END=10002481 GT:DP:GQ:MIN_DP:PL 0/0:56:0:50:0,0,731 621 20 10015548 . G <NON_REF> . . END=10015565 GT:DP:GQ:MIN_DP:PL 0/0:11:0:6:0,0,0 622 20 10015566 . G <NON_REF> . . END=10015580 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45 623 20 10015581 . G <NON_REF> . . END=10015598 GT:DP:GQ:MIN_DP:PL 0/0:2:6:2:0,6,69 1238 20 10098344 . A <NON_REF> . . END=10098344 GT:DP:GQ:MIN_DP:PL 0/0:4:0:4:0,0,1 1241 20 10098361 . T <NON_REF> . . END=10098380 GT:DP:GQ:MIN_DP:PL 0/0:1:0:1:0,0,0 1243 20 10098455 . A <NON_REF> . . END=10098551 GT:DP:GQ:MIN_DP:PL 0/0:0:0:0:0,0,0 [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/MethylationTypeCaller/
H A D	chr14_subset.methylC_seq.expected.vcf	2 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 chr14 3005640 . C T . . CONVERTED_BASE_COV=0;DP=1;REFERENCE_CONTEXT=CAA;UNCONVERTED_BASE_COV=1 GT .… 9 chr14 3005643 . C T . . CONVERTED_BASE_COV=0;DP=1;REFERENCE_CONTEXT=CCC;UNCONVERTED_BASE_COV=1 GT .… 10 chr14 3005654 . C T . . CONVERTED_BASE_COV=1;DP=1;REFERENCE_CONTEXT=CAC;UNCONVERTED_BASE_COV=0 GT .… 11 chr14 3005656 . C T . . CONVERTED_BASE_COV=1;DP=1;REFERENCE_CONTEXT=CTT;UNCONVERTED_BASE_COV=0 GT .… 12 chr14 3005659 . C T . . CONVERTED_BASE_COV=0;DP=1;REFERENCE_CONTEXT=CAC;UNCONVERTED_BASE_COV=1 GT .… 13 chr14 3005661 . C T . . CONVERTED_BASE_COV=1;DP=1;REFERENCE_CONTEXT=CAC;UNCONVERTED_BASE_COV=0 GT .… 14 chr14 3005663 . C T . . CONVERTED_BASE_COV=1;DP=1;REFERENCE_CONTEXT=CCA;UNCONVERTED_BASE_COV=0 GT .… 15 chr14 3005664 . C T . . CONVERTED_BASE_COV=1;DP=1;REFERENCE_CONTEXT=CAG;UNCONVERTED_BASE_COV=0 GT .… 16 chr14 3005668 . C T . . CONVERTED_BASE_COV=0;DP=1;REFERENCE_CONTEXT=CAG;UNCONVERTED_BASE_COV=1 GT .… [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/GnarlyGenotyper/
H A D	sample2.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 46 chr20 251411 . T <NON_REF> . . END=251411 GT:DP:GQ:MIN_DP:PL 0/0:25:6:25:0,6,700 48 chr20 251418 . A <NON_REF> . . END=251418 GT:DP:GQ:MIN_DP:PL 0/0:26:9:26:0,9,745 63 chr20 252896 . G <NON_REF> . . END=252896 GT:DP:GQ:MIN_DP:PL 0/0:26:8:26:0,8,693 65 chr20 252904 . A <NON_REF> . . END=252904 GT:DP:GQ:MIN_DP:PL 0/0:24:4:24:0,4,587 67 chr20 252908 . C <NON_REF> . . END=252908 GT:DP:GQ:MIN_DP:PL 0/0:25:5:25:0,5,679 69 chr20 252920 . T <NON_REF> . . END=252920 GT:DP:GQ:MIN_DP:PL 0/0:18:5:18:0,5,477 154 chr20 255805 . A <NON_REF> . . END=255817 GT:DP:GQ:MIN_DP:PL 0/0:11:6:9:0,6,90 205 chr20 257152 . C <NON_REF> . . END=257164 GT:DP:GQ:MIN_DP:PL 0/0:34:3:34:0,3,45 206 chr20 257173 . T <NON_REF> . . END=257174 GT:DP:GQ:MIN_DP:PL 0/0:36:3:36:0,3,45 [all …]
H A D	sample3.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 64 chr20 253859 . G <NON_REF> . . END=253859 GT:DP:GQ:MIN_DP:PL 0/0:25:5:25:0,5,669 82 chr20 255346 . G <NON_REF> . . END=255346 GT:DP:GQ:MIN_DP:PL 0/0:31:9:31:0,9,799 125 chr20 257173 . T <NON_REF> . . END=257174 GT:DP:GQ:MIN_DP:PL 0/0:28:3:28:0,3,45 130 chr20 257772 . T <NON_REF> . . END=257786 GT:DP:GQ:MIN_DP:PL 0/0:32:3:31:0,3,45 144 chr20 258662 . T <NON_REF> . . END=258664 GT:DP:GQ:MIN_DP:PL 0/0:26:9:24:0,9,675 231 chr20 263477 . G <NON_REF> . . END=263480 GT:DP:GQ:MIN_DP:PL 0/0:26:3:24:0,3,45 232 chr20 263485 . T <NON_REF> . . END=263496 GT:DP:GQ:MIN_DP:PL 0/0:23:3:22:0,3,45 315 chr20 278906 . G <NON_REF> . . END=278919 GT:DP:GQ:MIN_DP:PL 0/0:7:9:7:0,9,135 325 chr20 278967 . G <NON_REF> . . END=278980 GT:DP:GQ:MIN_DP:PL 0/0:9:6:7:0,6,154 [all …]
H A D	sample4.vcf	7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 48 chr20 251969 . A <NON_REF> . . END=251969 GT:DP:GQ:MIN_DP:PL 0/0:37:6:37:0,6,895 51 chr20 251981 . T <NON_REF> . . END=251981 GT:DP:GQ:MIN_DP:PL 0/0:39:8:39:0,8,915 175 chr20 255792 . T <NON_REF> . . END=255792 GT:DP:GQ:MIN_DP:PL 0/0:9:2:9:0,2,253 178 chr20 255804 . C <NON_REF> . . END=255817 GT:DP:GQ:MIN_DP:PL 0/0:9:2:9:0,2,135 508 chr20 278917 . G <NON_REF> . . END=278940 GT:DP:GQ:MIN_DP:PL 0/0:4:6:3:0,6,90 509 chr20 278942 . G <NON_REF> . . END=278955 GT:DP:GQ:MIN_DP:PL 0/0:4:6:3:0,6,90 623 chr20 288159 . T <NON_REF> . . END=288175 GT:DP:GQ:MIN_DP:PL 0/0:7:3:7:0,3,45 624 chr20 288177 . T <NON_REF> . . END=288179 GT:DP:GQ:MIN_DP:PL 0/0:5:3:5:0,3,45 625 chr20 288181 . T <NON_REF> . . END=288184 GT:DP:GQ:MIN_DP:PL 0/0:5:6:5:0,6,90 [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/walkers/CombineGVCFs/
H A D	twoSamples.MT.g.vcf	31 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 3463 MT 5656 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:9:9:0.728 ./.:4:3:-7.770e-01 3465 MT 5661 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:6:0.035 ./.:4:3:-7.770e-01 3467 MT 5663 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:7:6:-9.193e-01 ./.:5:5:0.010 3470 MT 5666 . T <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:7:6:-9.193e-01 ./.:5:5:0.305 3473 MT 5670 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:5:-8.445e-01 ./.:3:3:0.447 3474 MT 5671 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:5:-8.445e-01 ./.:3:3:0.646 3478 MT 5679 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:2:2:0.285 3480 MT 5681 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:3:3:0.504 3482 MT 5683 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:3:3:0.063 [all …]
H A D	NA19240.MT.filtered.g.vcf	29 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 160 MT 1 . G <NON_REF> . . END=2 GT:DP:MIN_DP:TLOD 0/0:66:47:-1.929e+00 161 MT 3 . T <NON_REF> . . END=3 GT:DP:MIN_DP:TLOD 0/0:121:121:-1.337e+00 162 MT 4 . C <NON_REF> . . END=6 GT:DP:MIN_DP:TLOD 0/0:205:166:-2.396e+00 163 MT 7 . A <NON_REF> . . END=7 GT:DP:MIN_DP:TLOD 0/0:289:289:-1.985e+00 164 MT 8 . G <NON_REF> . . END=8 GT:DP:MIN_DP:TLOD 0/0:337:337:-2.529e+00 2329 MT 5663 . C <NON_REF> . . END=5663 GT:DP:MIN_DP:TLOD 0/0:5:5:0.010 2332 MT 5666 . T <NON_REF> . . END=5666 GT:DP:MIN_DP:TLOD 0/0:5:5:0.305 2335 MT 5670 . A <NON_REF> . . END=5670 GT:DP:MIN_DP:TLOD 0/0:3:3:0.447 2336 MT 5671 . C <NON_REF> . . END=5671 GT:DP:MIN_DP:TLOD 0/0:3:3:0.646 [all …]
H A D	twoSamples.MT.vcf	31 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 3465 MT 5656 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:9:9:0.728 ./.:4:3:-7.770e-01 3467 MT 5661 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:6:0.035 ./.:4:3:-7.770e-01 3469 MT 5663 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:7:6:-9.193e-01 ./.:5:5:0.010 3472 MT 5666 . T <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:7:6:-9.193e-01 ./.:5:5:0.305 3475 MT 5670 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:5:-8.445e-01 ./.:3:3:0.447 3476 MT 5671 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:6:5:-8.445e-01 ./.:3:3:0.646 3480 MT 5679 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:2:2:0.285 3482 MT 5681 . C <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:3:3:0.504 3484 MT 5683 . A <NON_REF> . . . GT:DP:MIN_DP:TLOD ./.:4:2:-8.443e-01 ./.:3:3:0.063 [all …]
/dports/science/jmol/jmol-14.32.7/src/org/openscience/jmol/app/webexport/
H A D	Widgets.java	209 + GT.escapeHTML(GT.$("Animation")) in getJavaScript() 213 + GT.escapeHTML(GT.$("First Frame")) in getJavaScript() 219 + GT.escapeHTML(GT.$("Previous Frame")) in getJavaScript() 225 + GT.escapeHTML(GT.$("Play")) in getJavaScript() 231 + GT.escapeHTML(GT.$("Next Frame")) in getJavaScript() 237 + GT.escapeHTML(GT.$("Pause")) in getJavaScript() 243 + GT.escapeHTML(GT.$("Last Frame")) in getJavaScript() 251 + GT.escapeHTML(GT.$("Mode:")) in getJavaScript() 256 + GT.escapeHTML(GT.$("Loop")) in getJavaScript() 264 + GT.escapeHTML(GT.$("Palindrome")) in getJavaScript() [all …]
/dports/biology/bio-mocha/bcftools-1.14/test/
H A D	view.GT.vcf	`7 22 16050159 . C T 68 . . GT 0/0 0/1 0/0 8 22 16050252 . A T 85 . . GT 0/0 0/1 0/0 10 22 16051347 . G C 283 . . GT ./. 0/1 0/0 12 22 16051497 . A G 362 . . GT 1/1 0/1 0/0 13 22 16051968 . C A 136 . . GT 0/0 0/1 0/0 17 22 16052239 . A G 172 . . GT 0/0 0/1 0/0 18 22 16052513 . G C 153 . . GT 0/0 0/1 0/0 19 22 16052618 . G A 124 . . GT 0/0 0/1 0/0 20 22 16053659 . A C 352 . . GT 1/1 1/1 0/0 41 Y 16059973 . C A 195 . . GT 0 0 1 [all …]`
H A D	convert.gt.noHead.vcf	2 X 2698560 . G A . . . GT 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 3 X 2698630 . A G . . . GT 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 4 X 2698758 . CAA C . . . GT 0\|0 0\|1 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 28 X 2699555 . C A . . . GT 0 1 1 0 1 1\|1 1\|0 0\|1 0\|0 0\|1 29 X 2699645 . G T . . . GT 0 1 0 0 0 0\|0 0\|0 0\|1 0\|0 0\|0 30 X 2699676 . G A . . . GT 0 0 1 0 1 1\|0 1\|0 0\|0 0\|0 0\|1 31 X 2699728 . C T . . . GT 0 0 0 0 0 0\|0 0\|0 0\|0 0\|0 0\|0 32 X 2699775 . C A . . . GT 0 0 0 0 0 0\|0 0\|0 0\|0 0\|0 0\|0 33 X 2699898 . C CT . . . GT 0 0 1 0 1 1\|0 1\|0 0\|0 0\|0 0\|1 34 X 2699968 . A G . . . GT . 0 0 1 0 0\|1 0\|0 0\|0 0\|1 1\|0 [all …]
H A D	ad-bias.vcf	6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 22 16050159 . C T 68 . . GT:AD 0/0:4,0 0/1:6,8 0/0:26,0 9 22 16050252 . A T 85 . . GT:AD 0/0:3,0 0/1:13,13 0/0:40,0 10 22 16051249 . T C 32.1761 . . GT:AD 0/1:4,3 0/0:41,0 0/0:55,0 11 22 16051347 . G C 283 . . GT:AD 1/1:2,4 0/1:20,20 0/0:43,0 13 22 16051497 . A G 362 . . GT:AD 1/1:0,8 0/1:14,20 0/0:44,0 14 22 16051968 . C A 136 . . GT:AD 0/0:4,0 0/1:11,11 0/0:13,0 18 22 16052239 . A G 172 . . GT:AD 0/0:5,0 0/1:12,17 0/0:44,0 20 22 16052618 . G A 124 . . GT:AD 0/0:7,0 0/1:29,12 0/0:41,0 21 22 16053659 . A C 352 . . GT:AD 1/1:0,9 1/1:0,21 0/0:30,0 [all …]
/dports/biology/bcftools/bcftools-1.14/test/
H A D	view.GT.vcf	`7 22 16050159 . C T 68 . . GT 0/0 0/1 0/0 8 22 16050252 . A T 85 . . GT 0/0 0/1 0/0 10 22 16051347 . G C 283 . . GT ./. 0/1 0/0 12 22 16051497 . A G 362 . . GT 1/1 0/1 0/0 13 22 16051968 . C A 136 . . GT 0/0 0/1 0/0 17 22 16052239 . A G 172 . . GT 0/0 0/1 0/0 18 22 16052513 . G C 153 . . GT 0/0 0/1 0/0 19 22 16052618 . G A 124 . . GT 0/0 0/1 0/0 20 22 16053659 . A C 352 . . GT 1/1 1/1 0/0 41 Y 16059973 . C A 195 . . GT 0 0 1 [all …]`
H A D	convert.gt.noHead.vcf	2 X 2698560 . G A . . . GT 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 3 X 2698630 . A G . . . GT 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 4 X 2698758 . CAA C . . . GT 0\|0 0\|1 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 0\|0 28 X 2699555 . C A . . . GT 0 1 1 0 1 1\|1 1\|0 0\|1 0\|0 0\|1 29 X 2699645 . G T . . . GT 0 1 0 0 0 0\|0 0\|0 0\|1 0\|0 0\|0 30 X 2699676 . G A . . . GT 0 0 1 0 1 1\|0 1\|0 0\|0 0\|0 0\|1 31 X 2699728 . C T . . . GT 0 0 0 0 0 0\|0 0\|0 0\|0 0\|0 0\|0 32 X 2699775 . C A . . . GT 0 0 0 0 0 0\|0 0\|0 0\|0 0\|0 0\|0 33 X 2699898 . C CT . . . GT 0 0 1 0 1 1\|0 1\|0 0\|0 0\|0 0\|1 34 X 2699968 . A G . . . GT . 0 0 1 0 0\|1 0\|0 0\|0 0\|1 1\|0 [all …]
H A D	ad-bias.vcf	6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 8 22 16050159 . C T 68 . . GT:AD 0/0:4,0 0/1:6,8 0/0:26,0 9 22 16050252 . A T 85 . . GT:AD 0/0:3,0 0/1:13,13 0/0:40,0 10 22 16051249 . T C 32.1761 . . GT:AD 0/1:4,3 0/0:41,0 0/0:55,0 11 22 16051347 . G C 283 . . GT:AD 1/1:2,4 0/1:20,20 0/0:43,0 13 22 16051497 . A G 362 . . GT:AD 1/1:0,8 0/1:14,20 0/0:44,0 14 22 16051968 . C A 136 . . GT:AD 0/0:4,0 0/1:11,11 0/0:13,0 18 22 16052239 . A G 172 . . GT:AD 0/0:5,0 0/1:12,17 0/0:44,0 20 22 16052618 . G A 124 . . GT:AD 0/0:7,0 0/1:29,12 0/0:41,0 21 22 16053659 . A C 352 . . GT:AD 1/1:0,9 1/1:0,21 0/0:30,0 [all …]
/dports/biology/seqan-apps/seqan-seqan-v2.4.0/apps/bs_tools/tests/
H A D	snps_se_0.vcf	15 ##ID=<ID=GT,Number=1,Type=String,Description="Genotype"> 20 21 272 snp A G 46 PASS FB:9,0,7,0;RB=6,0,1,0; GT:DP:GS:MP 0\|1:23:42.9813:1 21 21 364 snp G A 46 PASS FB:6,0,12,0;RB=11,0,0,0; GT:DP:GS:MP 0\|1:29:36.4644:1 22 21 644 snp C T 46 PASS FB:0,1,0,11;RB=0,4,0,5; GT:DP:GS:MP 0\|1:21:33.4912:1 24 21 1032 snp T G 46 PASS FB:0,0,6,4;RB=2,0,1,3; GT:DP:GS:MP 0\|1:16:31.4388:1 25 21 1152 snp T A 46 PASS FB:9,0,0,4;RB=9,0,0,6; GT:DP:GS:MP 0\|1:28:56.2163:1 26 21 1379 snp T A 46 PASS FB:3,0,0,3;RB=9,0,0,8; GT:DP:GS:MP 0\|1:23:24.3217:1 29 21 1637 snp C T 46 PASS FB:0,0,0,8;RB=0,7,0,6; GT:DP:GS:MP 0\|1:22:39.9263:1 30 21 1752 snp T G 46 PASS FB:0,0,5,2;RB=3,0,0,2; GT:DP:GS:MP 0\|1:12:23.7543:1 34 21 2419 snp T G 46 PASS FB:0,0,3,4;RB=1,0,0,4; GT:DP:GS:MP 0\|1:12:18.042:1 [all …]
H A D	snps_se_1.vcf	15 ##ID=<ID=GT,Number=1,Type=String,Description="Genotype"> 20 21 272 snp A G 46 PASS FB:9,0,7,0;RB=6,0,1,0; GT:DP:GS:MP 0\|1:23:42.9813:1 21 21 364 snp G A 46 PASS FB:6,0,12,0;RB=11,0,0,0; GT:DP:GS:MP 0\|1:29:36.4644:1 22 21 644 snp C T 46 PASS FB:0,1,0,11;RB=0,4,0,5; GT:DP:GS:MP 0\|1:21:33.4912:1 24 21 1032 snp T G 46 PASS FB:0,0,6,4;RB=2,0,1,3; GT:DP:GS:MP 0\|1:16:31.4388:1 25 21 1152 snp T A 46 PASS FB:9,0,0,4;RB=9,0,0,6; GT:DP:GS:MP 0\|1:28:56.2163:1 26 21 1379 snp T A 46 PASS FB:3,0,0,3;RB=9,0,0,8; GT:DP:GS:MP 0\|1:23:24.3217:1 29 21 1637 snp C T 46 PASS FB:0,0,0,8;RB=0,7,0,6; GT:DP:GS:MP 0\|1:22:39.9263:1 30 21 1752 snp T G 46 PASS FB:0,0,5,2;RB=3,0,0,2; GT:DP:GS:MP 0\|1:12:23.7543:1 34 21 2419 snp T G 46 PASS FB:0,0,3,4;RB=1,0,0,4; GT:DP:GS:MP 0\|1:12:18.042:1 [all …]
/dports/biology/gatk/gatk-4.2.0.0/src/test/resources/org/broadinstitute/hellbender/tools/mutect/dream/vcfs/
H A D	sample_2.vcf	13 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 25 20 1182623 . G T 100 PASS SOMATIC;VAF=0.371428571429;DPR=35.0 GT 0/1 26 20 2136206 . T G 100 PASS SOMATIC;VAF=0.375;DPR=87.3333333333 GT 0/1 28 20 4567628 . G T 100 PASS SOMATIC;VAF=0.375;DPR=31.6666666667 GT 0/1 29 20 5056298 . G A 100 PASS SOMATIC;VAF=0.352941176471;DPR=19.0 GT 0/1 30 20 5407679 . A T 100 PASS SOMATIC;VAF=0.368421052632;DPR=38.0 GT 0/1 58 20 23479929 . C T 100 PASS SOMATIC;VAF=0.375;DPR=16.0 GT 0/1 65 20 32187832 . G A 100 PASS SOMATIC;VAF=0.36;DPR=29.0 GT 0/1 72 20 37616155 . G A 100 PASS SOMATIC;VAF=0.375;DPR=32.0 GT 0/1 81 20 42905450 . C G 100 PASS SOMATIC;VAF=0.375;DPR=16.0 GT 0/1 [all …]
H A D	sample_1.vcf	13 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> 23 20 2916255 . G C 100 PASS SOMATIC;VAF=0.5;DPR=20.0 GT 0/1 24 20 5270544 . C A 100 PASS SOMATIC;VAF=0.5;DPR=38.0 GT 0/1 26 20 6947936 . A G 100 PASS SOMATIC;VAF=0.5;DPR=32.0 GT 0/1 30 20 10022820 . A T 100 PASS SOMATIC;VAF=0.5;DPR=30.0 GT 0/1 33 20 14282738 . A C 100 PASS SOMATIC;VAF=0.5;DPR=14.0 GT 0/1 34 20 14331991 . T G 100 PASS SOMATIC;VAF=0.5;DPR=36.0 GT 0/1 35 20 14996613 . G A 100 PASS SOMATIC;VAF=0.5;DPR=34.0 GT 0/1 40 20 18338744 . T G 100 PASS SOMATIC;VAF=0.5;DPR=34.0 GT 0/1 44 20 20710460 . G T 100 PASS SOMATIC;VAF=0.5;DPR=30.0 GT 0/1 [all …]

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