Mercurial > repos > devteam > vcfannotate
annotate test-data/vcfannotate-test1.vcf @ 4:01e0321aca98 draft default tip
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/vcflib/vcfannotate commit 36e9065027cc7bf721e9d203208477ee88906c57"
author | iuc |
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date | Thu, 23 Jan 2020 08:03:53 -0500 (2020-01-23) |
parents | d64204113938 |
children |
rev | line source |
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0 | 1 ##fileformat=VCFv4.0 |
2 ##fileDate=20090805 | |
3 ##source=myImputationProgramV3.1 | |
4 ##reference=1000GenomesPilot-NCBI36 | |
5 ##phasing=partial | |
6 ##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data"> | |
7 ##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes"> | |
8 ##INFO=<ID=AC,Number=.,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed"> | |
9 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth"> | |
10 ##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency"> | |
11 ##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele"> | |
12 ##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129"> | |
13 ##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership"> | |
14 ##FILTER=<ID=q10,Description="Quality below 10"> | |
15 ##FILTER=<ID=s50,Description="Less than 50% of samples have data"> | |
16 ##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype"> | |
17 ##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality"> | |
18 ##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth"> | |
19 ##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality"> | |
20 ##ALT=<ID=DEL:ME:ALU,Description="Deletion of ALU element"> | |
21 ##ALT=<ID=CNV,Description="Copy number variable region"> | |
22 ##INFO=<ID=BED-features,Number=1,Type=String,Description="Annotation from /space/anton/galaxy-central/database/files/000/dataset_50.dat delimited by ':'"> | |
23 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA00001 NA00002 NA00003 | |
24 19 111 . A C 9.6 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 | |
25 19 112 . A G 10 . . GT:HQ 0|0:10,10 0|0:10,10 0/1:3,3 | |
26 20 14370 rs6054257 G A 29 PASS AF=0.5;DP=14;NS=3;DB;H2 GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,. | |
27 20 17330 . T A 3 q10 AF=0.017;DP=11;NS=3 GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3 0/0:41:3:.,. | |
28 20 1110696 rs6040355 A G,T 67 PASS AA=T;AF=0.333,0.667;BED-features=uc010zpo.2:uc002wel.4:uc010zpp.2:uc002wen.4;DP=10;NS=2;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2 2/2:35:4:.,. | |
29 20 1230237 . T . 47 PASS AA=T;DP=13;NS=3 GT:GQ:DP:HQ 0|0:54:.:56,60 0|0:48:4:51,51 0/0:61:2:.,. | |
30 20 1234567 microsat1 G GA,GAC 50 PASS AA=G;AC=3,1;AN=6;DP=9;NS=3 GT:GQ:DP 0/1:.:4 0/2:17:2 1/1:40:3 | |
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d64204113938
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tool_collections/vcflib/vcfannotate commit 0b9b6512272b82637c2f1e831367e89aed77ae79
devteam
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31 20 1235237 . T . 0 . . GT 0/0 0|0 ./. |
0 | 32 X 10 rsTest AC A,ATG 10 PASS . GT 0 0/1 0|2 |