Mercurial > repos > iuc > bcftools_plugin_setgt
diff test-data/cnv_baf_only.vcf @ 8:5ecd5f91b501 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit e648d86d550ddf2eb67237752320c390b3a780e5
| author | iuc |
|---|---|
| date | Wed, 05 Jun 2019 13:13:54 -0400 |
| parents | |
| children |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/cnv_baf_only.vcf Wed Jun 05 13:13:54 2019 -0400 @@ -0,0 +1,188 @@ +##fileformat=VCFv4.2 +##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> +##FORMAT=<ID=BAF,Number=1,Type=Float,Description="B Allele Frequency"> +#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT test +10 135656 rs10904561 T G . . . GT:BAF 0/1:0.5176 +10 135708 rs7917054 G A . . . GT:BAF 1/0:0.501 +10 178434 rs7089889 T G . . . GT:BAF 0/1:0.4833 +10 188805 rs12146291 A G . . . GT:BAF 0/1:0.4715 +10 203471 rs10903451 A G . . . GT:BAF 0/0:0.0000 +10 252693 rs2379078 T C . . . GT:BAF 0/0:0.0068 +10 273344 rs2448378 A C . . . GT:BAF 0/0:0.0000 +10 279248 rs2496278 C A . . . GT:BAF 1/0:0.6268 +10 291134 rs10508201 T C . . . GT:BAF 0/1:0.4723 +10 293358 exm2249181 A C . . . GT:BAF 0/0:0.0044 +10 313504 rs4880568 C T . . . GT:BAF 1/1:0.9803 +10 317501 rs2018975 C T . . . GT:BAF 0/0:0 +10 323283 rs3740304 A G . . . GT:BAF 0/1:0.5588 +10 326894 rs3125027 T C . . . GT:BAF 0/0:0.0005 +10 327162 exm805022 C T . . . GT:BAF 0/0:0 +10 329493 rs3815985 C A . . . GT:BAF 1/0:0.5187 +10 338553 rs3125031 C T . . . GT:BAF 1/0:0.4696 +10 354301 rs35198327 C T . . . GT:BAF 1/0:0.4929 +10 375475 variant.11341 C T . . . GT:BAF 0/0:0.000199999999999978 +10 377161 rs7070654 C T . . . GT:BAF 0/0:0 +10 387060 rs7904155 G A . . . GT:BAF 1/1:0.9945 +10 390962 exm805090 G A . . . GT:BAF 0/0:9.9999999999989e-05 +10 390983 exm805091 G A . . . GT:BAF 0/0:0 +10 394615 exm805105 G A . . . GT:BAF 0/0:0 +10 402390 exm805131 G C . . . GT:BAF 0/0:0.0000 +10 403792 exm805136 G C . . . GT:BAF 0/0:0.0000 +10 410501 exm805166 C T . . . GT:BAF 0/0:0 +10 413010 rs9787422 C T . . . GT:BAF 1/0:0.5334 +10 423555 rs12245012 G A . . . GT:BAF 0/0:0.00149999999999995 +10 423671 rs10904067 C T . . . GT:BAF 1/0:0.5566 +10 431161 exm2271240 C T . . . GT:BAF 1/0:0.4838 +10 435971 exm2249233 T C . . . GT:BAF 0/0:0.0000 +10 435990 exm805214 G A . . . GT:BAF 0/0:0 +10 453567 rs4881254 C T . . . GT:BAF 1/0:0.5079 +10 462885 rs10904173 G A . . . GT:BAF 1/0:0.4819 +10 465046 exm805254 G A . . . GT:BAF 0/0:0 +10 468599 rs12415961 T C . . . GT:BAF 0/1:0.5021 +10 486935 exm805280 G C . . . GT:BAF 0/0:0.0186 +10 487973 rs4881313 T C . . . GT:BAF 0/1:0.5628 +10 521431 exm2271370 C T . . . GT:BAF 1/1:0.9952 +10 521723 rs4881336 C T . . . GT:BAF 1/1:1 +10 547567 rs816599 A G . . . GT:BAF 1/1:1.0000 +10 554186 rs12251997 C T . . . GT:BAF 0/0:0.00309999999999999 +10 556129 rs10466270 A G . . . GT:BAF 0/1:0.5142 +10 566379 rs11252926 C T . . . GT:BAF 1/0:0.5024 +10 588406 rs10904450 A G . . . GT:BAF 0/0:0.0006 +10 592283 rs816646 G A . . . GT:BAF 1/0:0.5006 +10 601089 rs816650 C T . . . GT:BAF 0/0:0 +10 615782 rs17221309 G A . . . GT:BAF 0/0:0.00319999999999998 +10 635857 rs7069611 T C . . . GT:BAF 0/0:0.0013 +10 669358 rs7898821 G A . . . GT:BAF 0/0:0 +10 673037 rs816563 C T . . . GT:BAF 1/1:0.9065 +10 680428 rs2124585 G A . . . GT:BAF 1/0:0.5212 +10 712617 rs17136372 A C . . . GT:BAF 1/1:0.9992 +10 738630 rs1750792 C T . . . GT:BAF 0/0:0 +10 749238 rs553326 G T . . . GT:BAF 0/0:0.00229999999999997 +10 754033 rs2265090 C A . . . GT:BAF 0/0:0 +10 757222 rs10904546 A G . . . GT:BAF 0/0:0.0000 +10 766105 rs7906313 T C . . . GT:BAF 0/0:0.0116 +10 776027 rs11253377 C T . . . GT:BAF 1/1:0.9964 +10 787896 rs1769242 T C . . . GT:BAF 0/0:0.0000 +10 800213 rs2254501 G A . . . GT:BAF 1/1:0.9918 +10 802445 rs1769215 C T . . . GT:BAF 0/0:0.00370000000000004 +10 803721 rs2790381 C T . . . GT:BAF 1/1:0.9798 +10 811876 rs12414585 G A . . . GT:BAF 1/0:0.516 +10 813426 rs11253424 C T . . . GT:BAF 0/0:0 +10 815149 rs7084027 A G . . . GT:BAF 1/1:0.9944 +10 820868 rs10752019 C T . . . GT:BAF 0/0:0.0118 +10 833528 exm2271241 T G . . . GT:BAF 0/1:0.4896 +10 834736 rs4881530 G A . . . GT:BAF 0/0:0.00249999999999995 +10 836115 rs11253444 A G . . . GT:BAF 0/1:0.5199 +10 838179 rs1536337 T C . . . GT:BAF 0/0:0.0000 +10 858022 rs9124 C T . . . GT:BAF 0/0:0 +10 858924 exm805329 G A . . . GT:BAF 0/0:0 +10 859047 exm805338 C A . . . GT:BAF 0/0:0 +10 860687 exm805350 C T . . . GT:BAF 0/0:0 +10 860726 exm805354 T C . . . GT:BAF 0/0:0.0000 +10 860970 exm805360 A G . . . GT:BAF 0/0:0.0000 +10 871110 exm805378 G C . . . GT:BAF 0/0:0.0000 +10 871746 exm805386 G A . . . GT:BAF 0/0:0.00239999999999996 +10 875350 exm805392 G A . . . GT:BAF 0/0:0 +10 888899 exm805400 C T . . . GT:BAF 0/0:0.00470000000000004 +10 888916 exm805401 T C . . . GT:BAF 0/0:0.0000 +10 894838 rs12249828 C T . . . GT:BAF 1/0:0.4839 +10 903950 rs11253471 A G . . . GT:BAF 0/1:0.4747 +10 909757 exm805413 G A . . . GT:BAF 0/0:0 +10 909766 exm805415 G A . . . GT:BAF 0/0:0 +10 910074 exm805420 C T . . . GT:BAF 0/0:0.0071 +10 910081 exm805421 C T . . . GT:BAF 0/0:0.002 +10 927331 rs11253489 G A . . . GT:BAF 1/0:0.5325 +10 931618 exm805430 G A . . . GT:BAF 0/0:0 +10 931631 exm805431 C T . . . GT:BAF 0/0:0.00390000000000001 +11 135656 rs10904561 T G . . . GT:BAF 0/1:0.5176 +11 135708 rs7917054 G A . . . GT:BAF 1/0:0.501 +11 178434 rs7089889 T G . . . GT:BAF 0/1:0.4833 +11 188805 rs12146291 A G . . . GT:BAF 0/1:0.4715 +11 203471 rs10903451 A G . . . GT:BAF 0/0:0.0000 +11 252693 rs2379078 T C . . . GT:BAF 0/0:0.0068 +11 273344 rs2448378 A C . . . GT:BAF 0/0:0.0000 +11 279248 rs2496278 C A . . . GT:BAF 1/0:0.6268 +11 291134 rs10508201 T C . . . GT:BAF 0/1:0.4723 +11 293358 exm2249181 A C . . . GT:BAF 0/0:0.0044 +11 313504 rs4880568 C T . . . GT:BAF 1/1:0.9803 +11 317501 rs2018975 C T . . . GT:BAF 0/0:0 +11 323283 rs3740304 A G . . . GT:BAF 0/1:0.5588 +11 326894 rs3125027 T C . . . GT:BAF 0/0:0.0005 +11 327162 exm805022 C T . . . GT:BAF 0/0:0 +11 329493 rs3815985 C A . . . GT:BAF 1/0:0.5187 +11 338553 rs3125031 C T . . . GT:BAF 1/0:0.4696 +11 354301 rs35198327 C T . . . GT:BAF 1/0:0.4929 +11 375475 variant.11341 C T . . . GT:BAF 0/0:0.000199999999999978 +11 377161 rs7070654 C T . . . GT:BAF 0/0:0 +11 387060 rs7904155 G A . . . GT:BAF 1/1:0.9945 +11 390962 exm805090 G A . . . GT:BAF 0/0:9.9999999999989e-05 +11 390983 exm805091 G A . . . GT:BAF 0/0:0 +11 394615 exm805105 G A . . . GT:BAF 0/0:0 +11 402390 exm805131 G C . . . GT:BAF 0/0:0.0000 +11 403792 exm805136 G C . . . GT:BAF 0/0:0.0000 +11 410501 exm805166 C T . . . GT:BAF 0/0:0 +11 413010 rs9787422 C T . . . GT:BAF 1/0:0.5334 +11 423555 rs12245012 G A . . . GT:BAF 0/0:0.00149999999999995 +11 423671 rs10904067 C T . . . GT:BAF 1/0:0.5566 +11 431161 exm2271240 C T . . . GT:BAF 1/0:0.4838 +11 435971 exm2249233 T C . . . GT:BAF 0/0:0.0000 +11 435990 exm805214 G A . . . GT:BAF 0/0:0 +11 453567 rs4881254 C T . . . GT:BAF 1/0:0.5079 +11 462885 rs10904173 G A . . . GT:BAF 1/0:0.4819 +11 465046 exm805254 G A . . . GT:BAF 0/0:0 +11 468599 rs12415961 T C . . . GT:BAF 0/1:0.5021 +11 486935 exm805280 G C . . . GT:BAF 0/0:0.0186 +11 487973 rs4881313 T C . . . GT:BAF 0/1:0.5628 +11 521431 exm2271370 C T . . . GT:BAF 1/1:0.9952 +11 521723 rs4881336 C T . . . GT:BAF 1/1:1 +11 547567 rs816599 A G . . . GT:BAF 1/1:1.0000 +11 554186 rs12251997 C T . . . GT:BAF 0/0:0.00309999999999999 +11 556129 rs10466270 A G . . . GT:BAF 0/1:0.5142 +11 566379 rs11252926 C T . . . GT:BAF 1/0:0.5024 +11 588406 rs10904450 A G . . . GT:BAF 0/0:0.0006 +11 592283 rs816646 G A . . . GT:BAF 1/0:0.5006 +11 601089 rs816650 C T . . . GT:BAF 0/0:0 +11 615782 rs17221309 G A . . . GT:BAF 0/0:0.00319999999999998 +11 635857 rs7069611 T C . . . GT:BAF 0/0:0.0013 +11 669358 rs7898821 G A . . . GT:BAF 0/0:0 +11 673037 rs816563 C T . . . GT:BAF 1/1:0.9065 +11 680428 rs2124585 G A . . . GT:BAF 1/0:0.5212 +11 712617 rs17136372 A C . . . GT:BAF 1/1:0.9992 +11 738630 rs1750792 C T . . . GT:BAF 0/0:0 +11 749238 rs553326 G T . . . GT:BAF 0/0:0.00229999999999997 +11 754033 rs2265090 C A . . . GT:BAF 0/0:0 +11 757222 rs10904546 A G . . . GT:BAF 0/0:0.0000 +11 766105 rs7906313 T C . . . GT:BAF 0/0:0.0116 +11 776027 rs11253377 C T . . . GT:BAF 1/1:0.9964 +11 787896 rs1769242 T C . . . GT:BAF 0/0:0.0000 +11 800213 rs2254501 G A . . . GT:BAF 1/1:0.9918 +11 802445 rs1769215 C T . . . GT:BAF 0/0:0.00370000000000004 +11 803721 rs2790381 C T . . . GT:BAF 1/1:0.9798 +11 811876 rs12414585 G A . . . GT:BAF 1/0:0.516 +11 813426 rs11253424 C T . . . GT:BAF 0/0:0 +11 815149 rs7084027 A G . . . GT:BAF 1/1:0.9944 +11 820868 rs10752019 C T . . . GT:BAF 0/0:0.0118 +11 833528 exm2271241 T G . . . GT:BAF 0/1:0.4896 +11 834736 rs4881530 G A . . . GT:BAF 0/0:0.00249999999999995 +11 836115 rs11253444 A G . . . GT:BAF 0/1:0.5199 +11 838179 rs1536337 T C . . . GT:BAF 0/0:0.0000 +11 858022 rs9124 C T . . . GT:BAF 0/0:0 +11 858924 exm805329 G A . . . GT:BAF 0/0:0 +11 859047 exm805338 C A . . . GT:BAF 0/0:0 +11 860687 exm805350 C T . . . GT:BAF 0/0:0 +11 860726 exm805354 T C . . . GT:BAF 0/0:0.0000 +11 860970 exm805360 A G . . . GT:BAF 0/0:0.0000 +11 871110 exm805378 G C . . . GT:BAF 0/0:0.0000 +11 871746 exm805386 G A . . . GT:BAF 0/0:0.00239999999999996 +11 875350 exm805392 G A . . . GT:BAF 0/0:0 +11 888899 exm805400 C T . . . GT:BAF 0/0:0.00470000000000004 +11 888916 exm805401 T C . . . GT:BAF 0/0:0.0000 +11 894838 rs12249828 C T . . . GT:BAF 1/0:0.4839 +11 903950 rs11253471 A G . . . GT:BAF 0/1:0.4747 +11 909757 exm805413 G A . . . GT:BAF 0/0:0 +11 909766 exm805415 G A . . . GT:BAF 0/0:0 +11 910074 exm805420 C T . . . GT:BAF 0/0:0.0071 +11 910081 exm805421 C T . . . GT:BAF 0/0:0.002 +11 927331 rs11253489 G A . . . GT:BAF 1/0:0.5325 +11 931618 exm805430 G A . . . GT:BAF 0/0:0 +11 931631 exm805431 C T . . . GT:BAF 0/0:0.00390000000000001