Mercurial > repos > jjohnson > bcftools_plugin_missing2ref

annotate test-data/plugin1.vcf @ 0:ff65d6e0809b draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
author jjohnson
date Sat, 25 Jun 2016 20:51:04 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
1 ##fileformat=VCFv4.1
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
2 ##FILTER=<ID=PASS,Description="All filters passed">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
3 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
4 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
5 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
6 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
7 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
8 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
9 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
10 ##FILTER=<ID=q10,Description="Quality below 10">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
11 ##FILTER=<ID=test,Description="Testing filter">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
12 ##contig=<ID=1,assembly=b37,length=249250621>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
13 ##contig=<ID=2,assembly=b37,length=249250621>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
14 ##contig=<ID=3,assembly=b37,length=198022430>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
15 ##contig=<ID=4,assembly=b37,length=191154276>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
16 ##test=<ID=4,IE=5>
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
17 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
18 ##readme=AAAAAA
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
19 ##readme=BBBBBB
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
20 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
21 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
22 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
23 1 3000150 . C T 59.2 PASS . GT:GQ ./.:245 ./.:245
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
24 1 3000151 . C T 59.2 PASS . GT:DP:GQ ./.:32:245 ./.:32:245
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
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
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
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
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
27 1 3106154 . CAAA C 342 PASS . GT:GQ:DP ./.:245:32 ./.:245:32
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
28 1 3106154 . C CT 59.2 PASS . GT:GQ:DP ./.:245:32 ./.:245:32
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
29 1 3157410 . GA G 90.6 q10 . GT:GQ:DP 1/1:21:21 1/1:21:21
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
30 1 3162006 . GAA G 60.2 PASS . GT:GQ:DP ./.:212:22 ./.:212:22
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
31 1 3177144 . G T 45 PASS . GT:GQ:DP ./.:150:30 ./.:150:30
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
32 1 3177144 . G . 45 PASS . GT:GQ:DP ./.:150:30 ./.:150:30
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
33 1 3184885 . TAAAA TA,T 61.5 PASS . GT:GQ:DP ./.:12:10 ./.:12:10
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
34 2 3199812 . G GTT,GT 82.7 PASS . GT:GQ:DP ./.:322:26 ./.:322:26
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
35 3 3212016 . CTT C,CT 79 PASS . GT:GQ:DP ./.:91:26 ./.:91:26
ff65d6e0809b planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 21c66fb27c7e2fd21c7f7607b3b29e77e64fb86d-dirty
jjohnson
parents:
diff changeset
36 4 3258448 . TACACACAC T 59.9 PASS . GT:GQ:DP ./.:325:31 ./.:325:31