Mercurial > repos > iuc > snpeff_sars_cov_2

comparison test-data/input.vcf @ 0:2a3a00c1fa0a draft default tip

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/snpeff commit e6d1b32be9df14beb1e2859a0d2fa29a2d09227e"
author iuc
date Thu, 18 Jun 2020 16:11:49 -0400
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comparison
equal deleted inserted replaced
-1:000000000000 0:2a3a00c1fa0a
1 ##fileformat=VCFv4.0
2 ##fileDate=20200606
3 ##source=lofreq call --verbose --ref reference.fa --call-indels --min-cov 50 --max-depth 1000000 --min-bq 30 --min-alt-bq 30 --def-alt-bq 0 --min-mq 20 --max-mq 255 --min-jq 0 --min-alt-jq 0 --def-alt-jq 0 --sig 0.01 --bonf dynamic --no-default-filter -r NC_045512.2:1-14951 -o /data/dnb02/galaxy_db/job_working_directory/008/613/8613450/working/pp-tmp/lofreq2_call_paralleltqdqbfki/0.vcf.gz reads.bam
4 ##reference=reference.fa
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_snvqual_62,Description="Minimum SNV Quality (Phred) 62">
13 ##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
14 ##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
15 ##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
16 ##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65">
17 ##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
18 #CHROM POS ID REF ALT QUAL FILTER INFO
19 NC_045512.2 105 . G T 3155.0 PASS DP=748;AF=0.171123;SB=0;DP4=600,20,124,4
20 NC_045512.2 443 . GT G 99.0 PASS DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4
21 NC_045512.2 507 . ATGGTCATGTTATGGT A 100.0 PASS DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1
22 NC_045512.2 509 . GGTCATGTTATGGTT G 99.0 PASS DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2
23 NC_045512.2 514 . TGTTATG T 118.0 PASS DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1
24 NC_045512.2 515 . GTTATGGTT G 59.0 PASS DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2
25 NC_045512.2 517 . TATG T 91.0 PASS DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1
26 NC_045512.2 518 . ATG A 53.0 PASS DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1
27 NC_045512.2 518 . ATGGTT A 78.0 PASS DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1
28 NC_045512.2 685 . AAAGTCATTT A 60.0 PASS DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3
29 NC_045512.2 1011 . ATG A 77.0 PASS DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1
30 NC_045512.2 1135 . G GA 93.0 PASS DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5
31 NC_045512.2 1349 . C CA 257.0 PASS DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4
32 NC_045512.2 1730 . G A 116.0 PASS DP=997;AF=0.009027;SB=2;DP4=440,548,5,4
33 NC_045512.2 1946 . G GT 206.0 PASS DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4
34 NC_045512.2 2185 . G GT 73.0 PASS DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3
35 NC_045512.2 2310 . TA T 56.0 PASS DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3
36 NC_045512.2 2480 . A G 49314.0 PASS DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196
37 NC_045512.2 2558 . C T 49314.0 PASS DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402
38 NC_045512.2 2612 . G GT 58.0 PASS DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3
39 NC_045512.2 3259 . G T 69.0 PASS DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0
40 NC_045512.2 3412 . T TA 69.0 PASS DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5
41 NC_045512.2 3448 . C CA 59.0 PASS DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2
42 NC_045512.2 3545 . AATG A 57.0 PASS DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2
43 NC_045512.2 4148 . G GT 63.0 PASS DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4
44 NC_045512.2 6287 . TG T 60.0 PASS DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2
45 NC_045512.2 6696 . C CT 1002.0 PASS DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4
46 NC_045512.2 6696 . C T 141.0 PASS DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10
47 NC_045512.2 7504 . C CA 57.0 PASS DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3
48 NC_045512.2 9118 . C T 170.0 PASS DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11
49 NC_045512.2 9502 . C T 221.0 PASS DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12
50 NC_045512.2 9701 . AT A 59.0 PASS DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3
51 NC_045512.2 10605 . C CT 116.0 PASS DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4
52 NC_045512.2 10619 . C A 235.0 PASS DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13
53 NC_045512.2 10660 . TA T 122.0 PASS DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2
54 NC_045512.2 11074 . C CT 281.0 PASS DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8
55 NC_045512.2 11082 . TG T 1843.0 PASS DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1
56 NC_045512.2 11083 . G T 39536.0 PASS DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595
57 NC_045512.2 11133 . CT C 60.0 PASS DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4
58 NC_045512.2 11301 . TA T 104.0 PASS DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4
59 NC_045512.2 11812 . C CA 215.0 PASS DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3
60 NC_045512.2 11812 . C A 104.0 PASS DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9
61 NC_045512.2 12296 . C CA 222.0 PASS DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3
62 NC_045512.2 14110 . C CA 57.0 PASS DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3
63 NC_045512.2 14205 . A C 790.0 PASS DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9
64 NC_045512.2 14327 . C CA 59.0 PASS DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3
65 NC_045512.2 14432 . G GA 118.0 PASS DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5
66 NC_045512.2 14625 . C T 78.0 PASS DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3
67 NC_045512.2 14745 . TGAATTA T 111.0 PASS DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1
68 NC_045512.2 14805 . C T 49314.0 PASS DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398
69 NC_045512.2 14852 . TTGTA T 67.0 PASS DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3
70 NC_045512.2 17916 . AT A 53.0 PASS DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3
71 NC_045512.2 18350 . ATTTACC A 57.0 PASS DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3
72 NC_045512.2 18688 . T C 93.0 PASS DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2
73 NC_045512.2 19017 . C T 86.0 PASS DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6
74 NC_045512.2 19188 . A AT 55.0 PASS DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4
75 NC_045512.2 19983 . C CT 137.0 PASS DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6
76 NC_045512.2 20091 . C CA 81.0 PASS DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3
77 NC_045512.2 20296 . AAATT A 64.0 PASS DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3
78 NC_045512.2 20890 . G GT 63.0 PASS DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2
79 NC_045512.2 21101 . G GT 105.0 PASS DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6
80 NC_045512.2 22383 . C CT 64.0 PASS DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4
81 NC_045512.2 22583 . G GT 124.0 PASS DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5
82 NC_045512.2 22802 . C CA 87.0 PASS DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3
83 NC_045512.2 23191 . C T 5808.0 PASS DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96
84 NC_045512.2 23568 . GTA G 66.0 PASS DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1
85 NC_045512.2 23621 . G A 76.0 PASS DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5
86 NC_045512.2 23735 . G GA 53.0 PASS DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3
87 NC_045512.2 23835 . G GT 71.0 PASS DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5
88 NC_045512.2 24025 . ACTT A 76.0 PASS DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1
89 NC_045512.2 24358 . C CA 80.0 PASS DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4
90 NC_045512.2 24858 . G A 74.0 PASS DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4
91 NC_045512.2 24971 . G GT 61.0 PASS DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3
92 NC_045512.2 25703 . C CT 54.0 PASS DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4
93 NC_045512.2 26094 . TA T 78.0 PASS DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4
94 NC_045512.2 26144 . G T 33850.0 PASS DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519
95 NC_045512.2 27175 . C CT 63.0 PASS DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3
96 NC_045512.2 27481 . C T 96.0 PASS DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2
97 NC_045512.2 28147 . C CT 82.0 PASS DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4
98 NC_045512.2 28214 . C CT 307.0 PASS DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5
99 NC_045512.2 28214 . C T 95.0 PASS DP=891;AF=0.008979;SB=1;DP4=511,372,4,4
100 NC_045512.2 29003 . C A 70.0 PASS DP=953;AF=0.006296;SB=0;DP4=401,546,2,4
101 NC_045512.2 29304 . C CA 108.0 PASS DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3
102 NC_045512.2 29386 . C T 84.0 PASS DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0
103 NC_045512.2 29679 . CT C 70.0 PASS DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3