Mercurial > repos > iuc > ivar_variants

annotate test-data/zika/Z52_a.vcf @ 9:3888bbe7a9ca draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit f09d0bee3e957564beccb1bdb3610de02f639ec7"
author iuc
date Fri, 20 Aug 2021 20:33:21 +0000
parents 147465efa99c
children 38b91a3190cd
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6
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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1 ##fileformat=VCFv4.2
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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2 ##source=iVar
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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3 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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4 ##INFO=<ID=REF_DP,Number=1,Type=Integer,Description="Depth of reference base">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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5 ##INFO=<ID=REF_RV,Number=1,Type=Integer,Description="Depth of reference base on reverse reads">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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6 ##INFO=<ID=REF_QUAL,Number=1,Type=Integer,Description="Mean quality of reference base">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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7 ##INFO=<ID=ALT_DP,Number=1,Type=Integer,Description="Depth of alternate base">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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8 ##INFO=<ID=ALT_RV,Number=1,Type=Integer,Description="Deapth of alternate base on reverse reads">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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9 ##INFO=<ID=ALT_QUAL,Number=1,Type=Integer,Description="Mean quality of alternate base">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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10 ##INFO=<ID=AF,Number=1,Type=Float,Description="Frequency of alternate base">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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11 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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12 ##FILTER=<ID=PASS,Description="Result of p-value <= 0.05">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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13 ##FILTER=<ID=FAIL,Description="Result of p-value > 0.05">
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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14 #CHROM POS ID REF ALT QUAL FILTER INFO
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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25 PRV 5680 . C T . PASS DP=35;REF_DP=27;REF_RV=5;REF_QUAL=44;ALT_DP=8;ALT_RV=2;ALT_QUAL=46;AF=0.228571
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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
147465efa99c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ivar/ commit 847ec10cd36ea4f3cd4c257d5742f0fb401e364e"
iuc
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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