Mercurial > repos > jjohnson > bcftools_plugin_counts
comparison test-data/merge.c.vcf @ 0:17b407921818 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
| author | jjohnson |
|---|---|
| date | Sat, 25 Jun 2016 20:49:12 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:17b407921818 |
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| 1 ##fileformat=VCFv4.1 | |
| 2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag"> | |
| 3 ##INFO=<ID=TXT,Number=.,Type=String,Description="Testing in INFO"> | |
| 4 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\""> | |
| 5 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> | |
| 6 ##INFO=<ID=INTA,Number=A,Type=Integer,Description="Testing Number=A in INFO"> | |
| 7 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
| 8 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
| 9 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
| 10 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
| 11 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> | |
| 12 ##FILTER=<ID=q10,Description="Quality below 10"> | |
| 13 ##FILTER=<ID=test,Description="Testing filter"> | |
| 14 ##INFO=<ID=XRF,Number=R,Type=Float,Description="Test Number=AGR in INFO"> | |
| 15 ##INFO=<ID=XAF,Number=A,Type=Float,Description="Test Number=AGR in INFO"> | |
| 16 ##INFO=<ID=XGF,Number=G,Type=Float,Description="Test Number=AGR in INFO"> | |
| 17 ##INFO=<ID=XRI,Number=R,Type=Integer,Description="Test Number=AGR in INFO"> | |
| 18 ##INFO=<ID=XAI,Number=A,Type=Integer,Description="Test Number=AGR in INFO"> | |
| 19 ##INFO=<ID=XGI,Number=G,Type=Integer,Description="Test Number=AGR in INFO"> | |
| 20 ##INFO=<ID=XRS,Number=R,Type=String,Description="Test Number=AGR in INFO"> | |
| 21 ##INFO=<ID=XAS,Number=A,Type=String,Description="Test Number=AGR in INFO"> | |
| 22 ##INFO=<ID=XGS,Number=G,Type=String,Description="Test Number=AGR in INFO"> | |
| 23 ##contig=<ID=1,assembly=b37,length=249250621> | |
| 24 ##contig=<ID=3,assembly=b37,length=198022430> | |
| 25 ##contig=<ID=4,assembly=b37,length=191154276> | |
| 26 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta | |
| 27 ##readme=AAAAAA | |
| 28 ##readme=BBBBBB | |
| 29 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> | |
| 30 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
| 31 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT C D | |
| 32 1 3062915 id3D GTTT G 48.7 q10 TXT=BB;DP=999;DP4=4,3,2,1;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 | |
| 33 1 3062915 idSNP G C,T 419 test TEST=5;DP4=1,2,3,4;AN=4;AC=1,1;INTA=1,2 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 0/2:0,1:409:35:-20,-5,-20,-20,-5,-20 | |
| 34 1 3062915 id2D GTT G 999 q10 DP4=1,2,3,4;AN=4;AC=2 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20 | |
| 35 1 3106154 . CAAA C 72.6 PASS AN=0;AC=0 GT:GQ:DP .:245:32 ./.:245:32 | |
| 36 1 3106154 . C CT 459 PASS AN=4;AC=2 GT:GQ:DP 0/1:245:32 0/1:245:32 | |
| 37 1 3157410 . G T 46.7 q10 AN=4;AC=4 GT:GQ:DP 1/1:21:21 1/1:21:21 | |
| 38 1 3162006 . GAA GA 206 PASS AN=4;AC=2;XRF=1e6,5e5;XRI=1111,5555;XRS=AAA,DDD;XAF=5e5;XAI=5555;XAS=DDD;XGF=1e6,5e5,9e9;XGI=1111,5555,9999;XGS=A,E,F GT:GQ:DP 0/1:212:22 0/1:212:22 | |
| 39 1 3177144 . G . 364 PASS AN=4;AC=0 GT:GQ:DP 0/0:150:30 0/0:150:30 | |
| 40 1 3184885 . TAAAA TA,T 8.42 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:12:10 1/2:12:10 | |
| 41 2 3199812 . G GTT,GT 291 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:322:26 1/2:322:26 | |
| 42 3 3212016 . CTT C,CT 52.5 PASS AN=4;AC=2,2 GT:GQ:DP 1/2:91:26 1/2:91:26 | |
| 43 4 3258448 . TACACACAC T . PASS AN=4;AC=2 GT:GQ:DP 0/1:325:31 0/1:325:31 |