Mercurial > repos > iuc > bcftools_query
annotate test-data/isec.a.vcf @ 1:1fc5e47cb4a3 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit a9550d87541eda8b909e6aef1ad8cbf9e9e20d06
author | iuc |
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date | Wed, 13 Jul 2016 11:00:16 -0400 |
parents | 2fea169065ec |
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rev | line source |
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2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
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changeset
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1 ##fileformat=VCFv4.1 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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3 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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4 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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5 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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6 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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7 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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8 ##FILTER=<ID=q10,Description="Quality below 10"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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9 ##test=<xx=A,yy=B,zz=C> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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10 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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11 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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12 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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13 ##readme=AAAAAA |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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14 ##readme=BBBBBB |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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15 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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16 1 3062915 . GTTT G 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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17 1 3062915 . G T 1806 q10 DP=35;DP4=1,2,3,4;AN=2;AC=1 GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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18 1 3106154 . CAAA C 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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19 1 3106154 . C T,CT 1792 PASS DP=32;AN=2;AC=1 GT:GQ:DP 0/1:245:32 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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20 1 3157410 . GA G 628 q10 DP=21;AN=2;AC=2 GT:GQ:DP 1/1:21:21 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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21 1 3162006 . GAA G 1016 PASS DP=22;AN=2;AC=1 GT:GQ:DP 0/1:212:22 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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22 1 3177144 . GT G 727 PASS DP=30;AN=2;AC=1 GT:GQ:DP 0/1:150:30 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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23 1 3184885 . TAAAA TA,T 246 PASS DP=10;AN=2;AC=1,1 GT:GQ:DP 1/2:12:10 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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24 2 3199812 . G GTT,GT 481 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:322:26 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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25 3 3212016 . CTT C,CT 565 PASS DP=26;AN=2;AC=1,1 GT:GQ:DP 1/2:91:26 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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26 4 3212016 . TACACACAC T 325 PASS DP=31;AN=2;AC=1 GT:GQ:DP 0/1:325:31 |
2fea169065ec
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit ef90c4602bdb83ea7455946c9d175ea27284e643
iuc
parents:
diff
changeset
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27 4 3258448 . TACACACAC T 325 PASS DP=31;AN=2;AC=1 GT:GQ:DP 0/1:325:31 |