Mercurial > repos > iuc > ivar_removereads

comparison test-data/zika/Z52_a.vcf @ 15:69797fa273c3 draft

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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
comparison
equal deleted inserted replaced
14:f57ce5d5c997 15:69797fa273c3
7 ##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base"> 7 ##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">
8 ##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads"> 8 ##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">
9 ##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base"> 9 ##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">
10 ##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base"> 10 ##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">
11 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> 11 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
12 ##FILTER=<ID=PASS,Description="Result of p-value <= 0.05"> 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">
13 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05"> 13 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">
14 #CHROM POS ID REF ALT QUAL FILTER INFO 14 #CHROM POS ID REF ALT QUAL FILTER INFO
15 PRV 350 . A T . FAIL DP=106;REF_DP=101;REF_RV=101;REF_QUAL=36;ALT_DP=5;ALT_RV=5;ALT_QUAL=35;AF=0.0471698 15 PRV 350 . A T . FAIL DP=106;REF_DP=101;REF_RV=101;REF_QUAL=36;ALT_DP=5;ALT_RV=5;ALT_QUAL=35;AF=0.0471698;DP4=0,101,0,5
16 PRV 722 . C CA . FAIL DP=282;REF_DP=280;REF_RV=234;REF_QUAL=36;ALT_DP=9;ALT_RV=0;ALT_QUAL=20;AF=0.0319149;INDEL 16 PRV 722 . C CA . FAIL DP=282;REF_DP=280;REF_RV=234;REF_QUAL=36;ALT_DP=9;ALT_RV=0;ALT_QUAL=20;AF=0.0319149;INDEL;DP4=46,234,9,0
17 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 17 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
18 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 18 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
19 PRV 2702 . A G . FAIL DP=32;REF_DP=31;REF_RV=31;REF_QUAL=36;ALT_DP=1;ALT_RV=1;ALT_QUAL=23;AF=0.03125 19 PRV 2702 . A G . FAIL DP=32;REF_DP=31;REF_RV=31;REF_QUAL=36;ALT_DP=1;ALT_RV=1;ALT_QUAL=23;AF=0.03125;DP4=0,31,0,1
20 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 20 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
21 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 21 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
22 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 22 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
23 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 23 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
24 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 24 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
25 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 25 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
26 PRV 5723 . T G . FAIL DP=32;REF_DP=31;REF_RV=31;REF_QUAL=35;ALT_DP=1;ALT_RV=1;ALT_QUAL=21;AF=0.03125 26 PRV 5723 . T G . FAIL DP=32;REF_DP=31;REF_RV=31;REF_QUAL=35;ALT_DP=1;ALT_RV=1;ALT_QUAL=21;AF=0.03125;DP4=0,31,0,1
27 PRV 6201 . A G . FAIL DP=12;REF_DP=10;REF_RV=0;REF_QUAL=35;ALT_DP=2;ALT_RV=0;ALT_QUAL=38;AF=0.166667 27 PRV 6201 . A G . FAIL DP=12;REF_DP=10;REF_RV=0;REF_QUAL=35;ALT_DP=2;ALT_RV=0;ALT_QUAL=38;AF=0.166667;DP4=10,0,2,0
28 PRV 6211 . T C . FAIL DP=9;REF_DP=8;REF_RV=0;REF_QUAL=36;ALT_DP=1;ALT_RV=0;ALT_QUAL=35;AF=0.111111 28 PRV 6211 . T C . FAIL DP=9;REF_DP=8;REF_RV=0;REF_QUAL=36;ALT_DP=1;ALT_RV=0;ALT_QUAL=35;AF=0.111111;DP4=8,0,1,0
29 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 29 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
30 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 30 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