Mercurial > repos > iuc > bcftools_mpileup

annotate test-data/merge.4.a.vcf @ 7:f65383c7ed49 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 8f3fe2272c80fdb749db49be689681e4d1391bee"
author iuc
date Wed, 25 Dec 2019 12:24:37 -0500
parents 12f7c5315f7f
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.1
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
2 ##INFO=<ID=TEST,Number=1,Type=Integer,Description="Testing Tag">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
3 ##FORMAT=<ID=TT,Number=A,Type=Integer,Description="Testing Tag, with commas and \"escapes\" and escaped escapes combined with \\\"quotes\\\\\"">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
4 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
5 ##INFO=<ID=TR,Number=R,Type=Float,Description="Test tag">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
6 ##INFO=<ID=TA,Number=A,Type=Float,Description="Test tag">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
7 ##INFO=<ID=TG,Number=G,Type=Float,Description="Test tag">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
8 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
9 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
10 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
11 ##FORMAT=<ID=XR,Number=R,Type=Integer,Description="Some description">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
12 ##FORMAT=<ID=XA,Number=A,Type=Integer,Description="Some description">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
13 ##FORMAT=<ID=XG,Number=G,Type=Integer,Description="Some description">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
14 ##FORMAT=<ID=GL,Number=G,Type=Float,Description="Genotype Likelihood">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
15 ##FILTER=<ID=q10,Description="Quality below 10">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
16 ##FILTER=<ID=test,Description="Testing filter">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
17 ##contig=<ID=1,assembly=b37,length=249250621>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
18 ##contig=<ID=2,assembly=b37,length=249250621>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
19 ##contig=<ID=3,assembly=b37,length=198022430>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
20 ##contig=<ID=4,assembly=b37,length=191154276>
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
21 ##reference=file:///lustre/scratch105/projects/g1k/ref/main_project/human_g1k_v37.fasta
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
22 ##readme=AAAAAA
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
23 ##readme=BBBBBB
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
24 ##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
25 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
26 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
27 ##INFO=<ID=STR,Number=1,Type=String,Description="Test string type">
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
28 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT A B
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
29 1 3000000 id1 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GQ:XR:XA:XG 0/1:245:0,1:1:0,1,2 0/1:245:1,2:2:0,1,2
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
30 1 3000000 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ:XR:XA:XG 0/1:245:1,2:2:0,1,2 0/1:245:2,3:3:1,2,3
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
31 1 3000002 . C CCG 59.2 PASS AN=4;AC=2 GT:GQ 0/1:245 0/1:245
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
32 1 3000002 id2 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.:.:.
12f7c5315f7f planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 9d03fe38504a35d11660dadb44cb1beee32fcf4e
iuc
parents:
diff changeset
33 1 3000002 id3 C CCG 59.2 PASS AN=4;AC=2;TR=1,2;TA=1;TG=1,2,3 GT:GL:XR:XA:XG 0/1:245:.:.:. 0/1:245:.