Mercurial > repos > iuc > freyja_variants
comparison test-data/test.vcf @ 0:08c2d81e7942 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 2036e233d159a5c4b3b06ce6a681531259098f73
| author | iuc |
|---|---|
| date | Thu, 28 Jul 2022 09:26:32 +0000 |
| parents | |
| children |
comparison
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| -1:000000000000 | 0:08c2d81e7942 |
|---|---|
| 1 ##fileformat=VCFv4.0 | |
| 2 ##fileDate=20220125 | |
| 3 ##source=lofreq call -f freyja/data/NC_045512_Hu-1.fasta -o test.vcf freyja/data/test.bam | |
| 4 ##reference=freyja/data/NC_045512_Hu-1.fasta | |
| 5 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth"> | |
| 6 ##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency"> | |
| 7 ##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position"> | |
| 8 ##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases"> | |
| 9 ##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL."> | |
| 10 ##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant)."> | |
| 11 ##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position"> | |
| 12 ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10"> | |
| 13 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000"> | |
| 14 ##FILTER=<ID=min_snvqual_64,Description="Minimum SNV Quality (Phred) 64"> | |
| 15 ##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20"> | |
| 16 #CHROM POS ID REF ALT QUAL FILTER INFO | |
| 17 NC_045512.2 210 . G T 48519 PASS DP=3206;AF=0.500312;SB=13;DP4=585,1012,533,1071 | |
| 18 NC_045512.2 241 . C T 49314 PASS DP=3610;AF=0.497230;SB=9;DP4=580,1229,530,1265 | |
| 19 NC_045512.2 372 . A C 110 PASS DP=1369;AF=0.008766;SB=1;DP4=568,789,4,8 | |
| 20 NC_045512.2 441 . G A 105 PASS DP=2250;AF=0.007111;SB=2;DP4=893,1338,5,11 | |
| 21 NC_045512.2 1055 . G A 1592 PASS DP=300;AF=0.220000;SB=1;DP4=127,106,34,32 | |
| 22 NC_045512.2 1191 . C T 11391 PASS DP=850;AF=0.450588;SB=1;DP4=215,252,181,202 | |
| 23 NC_045512.2 1267 . C T 9741 PASS DP=577;AF=0.549393;SB=1;DP4=144,116,170,147 | |
| 24 NC_045512.2 2184 . A C 154 PASS DP=888;AF=0.014640;SB=1;DP4=768,107,11,2 | |
| 25 NC_045512.2 2973 . C T 1395 PASS DP=1368;AF=0.057749;SB=20;DP4=862,427,41,38 | |
| 26 NC_045512.2 3037 . C T 13537 PASS DP=1209;AF=0.401158;SB=0;DP4=209,511,139,346 | |
| 27 NC_045512.2 4897 . C T 159 PASS DP=431;AF=0.027842;SB=1;DP4=235,184,6,6 | |
| 28 NC_045512.2 5184 . C T 3943 PASS DP=347;AF=0.409222;SB=1;DP4=197,8,135,7 | |
| 29 NC_045512.2 5457 . C T 949 PASS DP=1254;AF=0.044657;SB=1;DP4=722,476,35,21 | |
| 30 NC_045512.2 6996 . T C 80 PASS DP=98;AF=0.040816;SB=0;DP4=48,46,2,2 | |
| 31 NC_045512.2 8782 . C T 32957 PASS DP=1458;AF=0.693416;SB=8;DP4=170,277,344,667 | |
| 32 NC_045512.2 8883 . T C 72 PASS DP=506;AF=0.015810;SB=6;DP4=113,384,0,8 | |
| 33 NC_045512.2 9203 . G A 10829 PASS DP=1088;AF=0.351103;SB=8;DP4=307,398,185,197 | |
| 34 NC_045512.2 9678 . T C 1593 PASS DP=109;AF=0.486239;SB=5;DP4=11,45,16,37 | |
| 35 NC_045512.2 11005 . C A 4808 PASS DP=467;AF=0.368308;SB=0;DP4=191,103,112,60 | |
| 36 NC_045512.2 11414 . C T 246 PASS DP=529;AF=0.030246;SB=6;DP4=398,115,10,6 | |
| 37 NC_045512.2 12235 . A C 117 PASS DP=603;AF=0.018242;SB=5;DP4=60,532,2,9 | |
| 38 NC_045512.2 12583 . T A 67 PASS DP=1093;AF=0.006404;SB=0;DP4=588,498,4,3 | |
| 39 NC_045512.2 14256 . A C 75 PASS DP=1404;AF=0.010684;SB=0;DP4=689,697,7,8 | |
| 40 NC_045512.2 14408 . C T 1357 PASS DP=108;AF=0.472222;SB=2;DP4=18,39,19,32 | |
| 41 NC_045512.2 16247 . C T 99 PASS DP=462;AF=0.021645;SB=2;DP4=283,169,5,5 | |
| 42 NC_045512.2 16255 . C T 77 PASS DP=464;AF=0.012931;SB=1;DP4=285,173,3,3 | |
| 43 NC_045512.2 17000 . C T 115 PASS DP=1044;AF=0.010536;SB=0;DP4=501,532,5,6 | |
| 44 NC_045512.2 17474 . C A 106 PASS DP=758;AF=0.015831;SB=1;DP4=405,341,6,6 | |
| 45 NC_045512.2 17496 . A G 6152 PASS DP=504;AF=0.430556;SB=0;DP4=88,199,67,150 | |
| 46 NC_045512.2 18060 . C T 14317 PASS DP=767;AF=0.598435;SB=2;DP4=24,284,41,418 | |
| 47 NC_045512.2 18096 . T C 125 PASS DP=161;AF=0.043478;SB=1;DP4=59,95,2,5 | |
| 48 NC_045512.2 18311 . T C 121 PASS DP=869;AF=0.011507;SB=16;DP4=432,427,1,9 | |
| 49 NC_045512.2 18395 . C T 82 PASS DP=1038;AF=0.009634;SB=1;DP4=568,456,5,5 | |
| 50 NC_045512.2 19547 . C T 851 PASS DP=863;AF=0.054461;SB=0;DP4=409,407,24,23 | |
| 51 NC_045512.2 20396 . A G 489 PASS DP=32;AF=0.500000;SB=0;DP4=14,2,14,2 | |
| 52 NC_045512.2 21618 . C G 375 PASS DP=40;AF=0.375000;SB=1;DP4=15,9,11,4 | |
| 53 NC_045512.2 21792 . A C 4658 PASS DP=477;AF=0.354298;SB=0;DP4=154,154,83,86 | |
| 54 NC_045512.2 21849 . A C 75 PASS DP=288;AF=0.017361;SB=2;DP4=41,239,1,4 | |
| 55 NC_045512.2 21974 . G T 82 PASS DP=168;AF=0.029762;SB=0;DP4=59,104,2,3 | |
| 56 NC_045512.2 21987 . G A 4045 PASS DP=333;AF=0.420420;SB=0;DP4=93,100,68,72 | |
| 57 NC_045512.2 22009 . C A 330 PASS DP=333;AF=0.060060;SB=0;DP4=151,162,10,10 | |
| 58 NC_045512.2 22206 . A G 1045 PASS DP=341;AF=0.131965;SB=0;DP4=142,153,21,24 | |
| 59 NC_045512.2 22296 . A G 103 PASS DP=518;AF=0.015444;SB=3;DP4=340,167,4,4 | |
| 60 NC_045512.2 22482 . C T 79 PASS DP=158;AF=0.031646;SB=0;DP4=51,102,2,3 | |
| 61 NC_045512.2 22995 . C A 3384 PASS DP=222;AF=0.504505;SB=0;DP4=60,50,61,51 | |
| 62 NC_045512.2 23403 . A G 6370 PASS DP=556;AF=0.395683;SB=10;DP4=166,169,126,94 | |
| 63 NC_045512.2 23525 . C T 125 PASS DP=358;AF=0.025140;SB=0;DP4=67,282,1,8 | |
| 64 NC_045512.2 23601 . C T 66 PASS DP=957;AF=0.009404;SB=1;DP4=427,520,5,4 | |
| 65 NC_045512.2 23604 . C G 13373 PASS DP=959;AF=0.488008;SB=0;DP4=220,271,211,257 | |
| 66 NC_045512.2 23607 . G T 532 PASS DP=958;AF=0.037578;SB=0;DP4=412,506,17,19 | |
| 67 NC_045512.2 23618 . A G 83 PASS DP=959;AF=0.011470;SB=0;DP4=424,524,5,6 | |
| 68 NC_045512.2 24410 . G A 267 PASS DP=22;AF=0.409091;SB=0;DP4=4,9,3,6 | |
| 69 NC_045512.2 24780 . A G 84 PASS DP=707;AF=0.012730;SB=2;DP4=316,382,3,6 | |
| 70 NC_045512.2 25469 . C T 10803 PASS DP=1085;AF=0.355760;SB=1;DP4=210,488,111,275 | |
| 71 NC_045512.2 25606 . G A 64 PASS DP=2215;AF=0.005418;SB=0;DP4=1181,1016,6,6 | |
| 72 NC_045512.2 26542 . C T 362 PASS DP=78;AF=0.179487;SB=6;DP4=41,23,6,8 | |
| 73 NC_045512.2 26767 . T C 5916 PASS DP=531;AF=0.384181;SB=3;DP4=219,108,130,74 | |
| 74 NC_045512.2 27752 . C T 2820 PASS DP=415;AF=0.260241;SB=18;DP4=184,123,79,29 | |
| 75 NC_045512.2 27920 . C T 167 PASS DP=2351;AF=0.008932;SB=0;DP4=1543,786,14,7 | |
| 76 NC_045512.2 27924 . A C 1081 PASS DP=2351;AF=0.030200;SB=0;DP4=1511,768,46,25 | |
| 77 NC_045512.2 28144 . T C 17994 PASS DP=669;AF=0.792227;SB=22;DP4=45,94,243,287 | |
| 78 NC_045512.2 28253 . C T 5868 PASS DP=471;AF=0.430998;SB=217;DP4=15,251,86,117 | |
| 79 NC_045512.2 28387 . A C 109 PASS DP=1287;AF=0.012432;SB=6;DP4=1141,129,13,3 | |
| 80 NC_045512.2 28461 . A G 29706 PASS DP=2257;AF=0.443952;SB=1;DP4=688,565,540,462 | |
| 81 NC_045512.2 28698 . C A 7287 PASS DP=544;AF=0.455882;SB=0;DP4=180,114,151,97 | |
| 82 NC_045512.2 28836 . C T 102 PASS DP=815;AF=0.011043;SB=0;DP4=495,310,6,3 | |
| 83 NC_045512.2 28851 . G T 72 PASS DP=815;AF=0.009816;SB=3;DP4=497,310,4,4 | |
| 84 NC_045512.2 28853 . T A 2280 PASS DP=817;AF=0.124847;SB=3;DP4=441,273,59,43 | |
| 85 NC_045512.2 28881 . G T 9326 PASS DP=721;AF=0.443828;SB=2;DP4=221,180,183,137 | |
| 86 NC_045512.2 29402 . G T 30263 PASS DP=1934;AF=0.512410;SB=45;DP4=700,243,814,177 | |
| 87 NC_045512.2 29512 . T C 44232 PASS DP=2655;AF=0.554802;SB=7;DP4=670,511,797,676 | |
| 88 NC_045512.2 29581 . T C 227 PASS DP=2170;AF=0.011982;SB=0;DP4=1905,221,24,2 | |
| 89 NC_045512.2 29742 . G T 1184 PASS DP=60;AF=0.616667;SB=0;DP4=7,16,11,26 |