Mercurial > repos > iuc > ivar_removereads

annotate test-data/zika/Z52_a_pass.vcf @ 15:69797fa273c3 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/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
author iuc
date Tue, 27 Jun 2023 17:12:25 +0000
parents 7f1cfa4c0e32
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
7
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
1 ##fileformat=VCFv4.2
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
2 ##source=iVar
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
4 ##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
5 ##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
6 ##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
7 ##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
8 ##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
9 ##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
10 ##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
11 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
15
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
12 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">
7
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
13 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">
43aac8d29685 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 80ad6146e8852fb04fbdbe7b14ab120eee605e3a"
iuc
parents:
diff changeset
14 #CHROM POS ID REF ALT QUAL FILTER INFO
15
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
15 PRV 1682 . C T . PASS DP=1133;REF_DP=1097;REF_RV=984;REF_QUAL=37;ALT_DP=34;ALT_RV=33;ALT_QUAL=37;AF=0.0300088;DP4=113,984,1,33
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
16 PRV 1965 . T G . PASS DP=365;REF_DP=302;REF_RV=113;REF_QUAL=37;ALT_DP=63;ALT_RV=25;ALT_QUAL=37;AF=0.172603;DP4=189,113,38,25
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
17 PRV 2781 . T G . PASS DP=408;REF_DP=354;REF_RV=70;REF_QUAL=37;ALT_DP=48;ALT_RV=8;ALT_QUAL=36;AF=0.117647;DP4=284,70,40,8
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
18 PRV 2922 . C T . PASS DP=275;REF_DP=264;REF_RV=0;REF_QUAL=36;ALT_DP=11;ALT_RV=0;ALT_QUAL=36;AF=0.04;DP4=264,0,11,0
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
19 PRV 3148 . Y T . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=1324;ALT_RV=264;ALT_QUAL=36;AF=0.77563;DP4=0,0,1060,264
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
20 PRV 3148 . Y C . PASS DP=1707;REF_DP=0;REF_RV=0;REF_QUAL=0;ALT_DP=381;ALT_RV=75;ALT_QUAL=36;AF=0.223199;DP4=0,0,306,75
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
21 PRV 3295 . A G . PASS DP=1040;REF_DP=1002;REF_RV=1002;REF_QUAL=35;ALT_DP=38;ALT_RV=38;ALT_QUAL=33;AF=0.0365385;DP4=0,1002,0,38
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
22 PRV 5680 . C T . PASS DP=35;REF_DP=27;REF_RV=10;REF_QUAL=44;ALT_DP=8;ALT_RV=3;ALT_QUAL=46;AF=0.228571;DP4=17,10,5,3
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
23 PRV 7916 . C T . PASS DP=432;REF_DP=351;REF_RV=289;REF_QUAL=36;ALT_DP=81;ALT_RV=78;ALT_QUAL=37;AF=0.1875;DP4=62,289,3,78
69797fa273c3 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 9d25797b06335056930bddede98a2f3f9a303470
iuc
parents: 11
diff changeset
24 PRV 9713 . C T . PASS DP=387;REF_DP=374;REF_RV=0;REF_QUAL=37;ALT_DP=13;ALT_RV=0;ALT_QUAL=35;AF=0.0335917;DP4=374,0,13,0