Mercurial > repos > jjohnson > bcftools_roh

annotate test-data/plugin1.vcf @ 1:357ef9b26247 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sun, 26 Jun 2016 15:44:01 -0400
parents ee03050edc3d
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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1 ##fileformat=VCFv4.1
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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2 ##FILTER=<ID=PASS,Description="All filters passed">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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3 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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4 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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5 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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8 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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9 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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10 ##FILTER=<ID=q10,Description="Quality below 10">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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11 ##FILTER=<ID=test,Description="Testing filter">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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12 ##contig=<ID=1,assembly=b37,length=249250621>
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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13 ##contig=<ID=2,assembly=b37,length=249250621>
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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14 ##contig=<ID=3,assembly=b37,length=198022430>
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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15 ##contig=<ID=4,assembly=b37,length=191154276>
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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16 ##test=<ID=4,IE=5>
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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17 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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18 ##readme=AAAAAA
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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19 ##readme=BBBBBB
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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20 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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21 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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23 1 3000150 . C T 59.2 PASS . GT:GQ ./.:245 ./.:245
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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24 1 3000151 . C T 59.2 PASS . GT:DP:GQ ./.:32:245 ./.:32:245
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
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25 1 3062915 id3D GTTT G 12.9 q10 DP4=1,2,3,4;INDEL;STR=test GT:GQ:DP:GL 0/1:409:35:-20,-5,-20 0/1:409:35:-20,-5,-20
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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26 1 3062915 idSNP G T,C 12.6 test TEST=5;DP4=1,2,3,4 GT:TT:GQ:DP:GL 0/1:0,1:409:35:-20,-5,-20,-20,-5,-20 2:0,1:409:35:-20,-5,-20
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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27 1 3106154 . CAAA C 342 PASS . GT:GQ:DP ./.:245:32 ./.:245:32
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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28 1 3106154 . C CT 59.2 PASS . GT:GQ:DP ./.:245:32 ./.:245:32
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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29 1 3157410 . GA G 90.6 q10 . GT:GQ:DP 1/1:21:21 1/1:21:21
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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30 1 3162006 . GAA G 60.2 PASS . GT:GQ:DP ./.:212:22 ./.:212:22
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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31 1 3177144 . G T 45 PASS . GT:GQ:DP ./.:150:30 ./.:150:30
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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32 1 3177144 . G . 45 PASS . GT:GQ:DP ./.:150:30 ./.:150:30
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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33 1 3184885 . TAAAA TA,T 61.5 PASS . GT:GQ:DP ./.:12:10 ./.:12:10
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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34 2 3199812 . G GTT,GT 82.7 PASS . GT:GQ:DP ./.:322:26 ./.:322:26
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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35 3 3212016 . CTT C,CT 79 PASS . GT:GQ:DP ./.:91:26 ./.:91:26
ee03050edc3d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
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36 4 3258448 . TACACACAC T 59.9 PASS . GT:GQ:DP ./.:325:31 ./.:325:31