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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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##fileformat=VCFv4.0
##fileDate=20200606
##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 
##reference=reference.fa
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw Depth">
##INFO=<ID=AF,Number=1,Type=Float,Description="Allele Frequency">
##INFO=<ID=SB,Number=1,Type=Integer,Description="Phred-scaled strand bias at this position">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="Counts for ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=CONSVAR,Number=0,Type=Flag,Description="Indicates that the variant is a consensus variant (as opposed to a low frequency variant).">
##INFO=<ID=HRUN,Number=1,Type=Integer,Description="Homopolymer length to the right of report indel position">
##FILTER=<ID=min_snvqual_62,Description="Minimum SNV Quality (Phred) 62">
##FILTER=<ID=min_indelqual_50,Description="Minimum Indel Quality (Phred) 50">
##FILTER=<ID=min_dp_10,Description="Minimum Coverage 10">
##FILTER=<ID=sb_fdr,Description="Strand-Bias Multiple Testing Correction: fdr corr. pvalue > 0.001000">
##FILTER=<ID=min_snvqual_65,Description="Minimum SNV Quality (Phred) 65">
##FILTER=<ID=min_indelqual_53,Description="Minimum Indel Quality (Phred) 53">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
NC_045512.2	105	.	G	T	3155.0	PASS	DP=748;AF=0.171123;SB=0;DP4=600,20,124,4
NC_045512.2	443	.	GT	G	99.0	PASS	DP=1286;AF=0.004666;SB=0;DP4=718,586,3,3;INDEL;HRUN=4
NC_045512.2	507	.	ATGGTCATGTTATGGT	A	100.0	PASS	DP=1554;AF=0.003861;SB=10;DP4=684,865,5,1;INDEL;HRUN=1
NC_045512.2	509	.	GGTCATGTTATGGTT	G	99.0	PASS	DP=1567;AF=0.003829;SB=0;DP4=706,873,3,3;INDEL;HRUN=2
NC_045512.2	514	.	TGTTATG	T	118.0	PASS	DP=1696;AF=0.004127;SB=1;DP4=865,826,3,4;INDEL;HRUN=1
NC_045512.2	515	.	GTTATGGTT	G	59.0	PASS	DP=1706;AF=0.002345;SB=4;DP4=887,826,1,3;INDEL;HRUN=2
NC_045512.2	517	.	TATG	T	91.0	PASS	DP=1733;AF=0.003462;SB=15;DP4=882,856,6,0;INDEL;HRUN=1
NC_045512.2	518	.	ATG	A	53.0	PASS	DP=1679;AF=0.002382;SB=4;DP4=892,842,1,3;INDEL;HRUN=1
NC_045512.2	518	.	ATGGTT	A	78.0	PASS	DP=1679;AF=0.002978;SB=1;DP4=892,842,2,3;INDEL;HRUN=1
NC_045512.2	685	.	AAAGTCATTT	A	60.0	PASS	DP=1188;AF=0.003367;SB=2;DP4=607,618,1,3;INDEL;HRUN=3
NC_045512.2	1011	.	ATG	A	77.0	PASS	DP=1345;AF=0.003717;SB=1;DP4=927,454,3,2;INDEL;HRUN=1
NC_045512.2	1135	.	G	GA	93.0	PASS	DP=1272;AF=0.004717;SB=3;DP4=663,650,2,4;INDEL;HRUN=5
NC_045512.2	1349	.	C	CA	257.0	PASS	DP=1121;AF=0.011597;SB=1;DP4=444,668,6,7;INDEL;HRUN=4
NC_045512.2	1730	.	G	A	116.0	PASS	DP=997;AF=0.009027;SB=2;DP4=440,548,5,4
NC_045512.2	1946	.	G	GT	206.0	PASS	DP=1976;AF=0.006073;SB=0;DP4=982,986,6,6;INDEL;HRUN=4
NC_045512.2	2185	.	G	GT	73.0	PASS	DP=2095;AF=0.002387;SB=4;DP4=1374,803,2,3;INDEL;HRUN=3
NC_045512.2	2310	.	TA	T	56.0	PASS	DP=2134;AF=0.001874;SB=2;DP4=1056,1084,1,3;INDEL;HRUN=3
NC_045512.2	2480	.	A	G	49314.0	PASS	DP=2088;AF=0.986590;SB=3;DP4=1,0,890,1196
NC_045512.2	2558	.	C	T	49314.0	PASS	DP=2141;AF=0.983652;SB=0;DP4=0,1,736,1402
NC_045512.2	2612	.	G	GT	58.0	PASS	DP=1770;AF=0.002260;SB=4;DP4=884,972,3,1;INDEL;HRUN=3
NC_045512.2	3259	.	G	T	69.0	PASS	DP=1704;AF=0.004108;SB=25;DP4=723,974,7,0
NC_045512.2	3412	.	T	TA	69.0	PASS	DP=1670;AF=0.002994;SB=0;DP4=803,866,2,3;INDEL;HRUN=5
NC_045512.2	3448	.	C	CA	59.0	PASS	DP=1732;AF=0.002309;SB=0;DP4=733,997,2,2;INDEL;HRUN=2
NC_045512.2	3545	.	AATG	A	57.0	PASS	DP=2002;AF=0.001998;SB=4;DP4=945,1062,3,1;INDEL;HRUN=2
NC_045512.2	4148	.	G	GT	63.0	PASS	DP=1147;AF=0.003487;SB=1;DP4=474,683,1,3;INDEL;HRUN=4
NC_045512.2	6287	.	TG	T	60.0	PASS	DP=1537;AF=0.002602;SB=2;DP4=810,729,3,1;INDEL;HRUN=2
NC_045512.2	6696	.	C	CT	1002.0	PASS	DP=1985;AF=0.022670;SB=1;DP4=739,1238,18,27;INDEL;HRUN=4
NC_045512.2	6696	.	C	T	141.0	PASS	DP=2023;AF=0.006920;SB=0;DP4=752,1256,5,10
NC_045512.2	7504	.	C	CA	57.0	PASS	DP=1874;AF=0.002134;SB=0;DP4=990,903,2,2;INDEL;HRUN=3
NC_045512.2	9118	.	C	T	170.0	PASS	DP=2259;AF=0.006640;SB=14;DP4=1213,1031,4,11
NC_045512.2	9502	.	C	T	221.0	PASS	DP=2082;AF=0.009606;SB=0;DP4=836,1225,8,12
NC_045512.2	9701	.	AT	A	59.0	PASS	DP=1741;AF=0.002298;SB=2;DP4=843,930,1,3;INDEL;HRUN=3
NC_045512.2	10605	.	C	CT	116.0	PASS	DP=2586;AF=0.003094;SB=0;DP4=1507,1082,5,3;INDEL;HRUN=4
NC_045512.2	10619	.	C	A	235.0	PASS	DP=2564;AF=0.007800;SB=5;DP4=1272,1272,7,13
NC_045512.2	10660	.	TA	T	122.0	PASS	DP=2326;AF=0.003439;SB=15;DP4=1292,1057,1,7;INDEL;HRUN=2
NC_045512.2	11074	.	C	CT	281.0	PASS	DP=1459;AF=0.036326;SB=2;DP4=822,613,28,25;INDEL;HRUN=8
NC_045512.2	11082	.	TG	T	1843.0	PASS	DP=1309;AF=0.058060;SB=0;DP4=662,589,39,37;INDEL;HRUN=1
NC_045512.2	11083	.	G	T	39536.0	PASS	DP=1319;AF=0.918120;SB=0;DP4=0,0,645,595
NC_045512.2	11133	.	CT	C	60.0	PASS	DP=1181;AF=0.003387;SB=2;DP4=607,573,3,1;INDEL;HRUN=4
NC_045512.2	11301	.	TA	T	104.0	PASS	DP=2098;AF=0.003337;SB=9;DP4=796,1299,5,2;INDEL;HRUN=4
NC_045512.2	11812	.	C	CA	215.0	PASS	DP=2020;AF=0.005941;SB=0;DP4=891,1127,5,7;INDEL;HRUN=3
NC_045512.2	11812	.	C	A	104.0	PASS	DP=2030;AF=0.004926;SB=13;DP4=895,1123,1,9
NC_045512.2	12296	.	C	CA	222.0	PASS	DP=1709;AF=0.007022;SB=6;DP4=573,1131,6,6;INDEL;HRUN=3
NC_045512.2	14110	.	C	CA	57.0	PASS	DP=1940;AF=0.002062;SB=0;DP4=872,1128,2,2;INDEL;HRUN=3
NC_045512.2	14205	.	A	C	790.0	PASS	DP=2047;AF=0.023449;SB=38;DP4=1106,890,41,9
NC_045512.2	14327	.	C	CA	59.0	PASS	DP=1729;AF=0.002313;SB=0;DP4=693,1040,2,2;INDEL;HRUN=3
NC_045512.2	14432	.	G	GA	118.0	PASS	DP=1895;AF=0.004222;SB=3;DP4=1004,913,3,5;INDEL;HRUN=5
NC_045512.2	14625	.	C	T	78.0	PASS	DP=2695;AF=0.003340;SB=3;DP4=2134,550,7,3
NC_045512.2	14745	.	TGAATTA	T	111.0	PASS	DP=2063;AF=0.003393;SB=8;DP4=975,1086,1,6;INDEL;HRUN=1
NC_045512.2	14805	.	C	T	49314.0	PASS	DP=2660;AF=0.987594;SB=0;DP4=0,0,1259,1398
NC_045512.2	14852	.	TTGTA	T	67.0	PASS	DP=2763;AF=0.001810;SB=1;DP4=1578,1259,2,3;INDEL;HRUN=3
NC_045512.2	17916	.	AT	A	53.0	PASS	DP=2304;AF=0.001736;SB=4;DP4=1310,1011,1,3;INDEL;HRUN=3
NC_045512.2	18350	.	ATTTACC	A	57.0	PASS	DP=1950;AF=0.002051;SB=0;DP4=974,1048,2,2;INDEL;HRUN=3
NC_045512.2	18688	.	T	C	93.0	PASS	DP=1875;AF=0.005333;SB=9;DP4=938,925,8,2
NC_045512.2	19017	.	C	T	86.0	PASS	DP=2058;AF=0.004373;SB=1;DP4=910,1138,3,6
NC_045512.2	19188	.	A	AT	55.0	PASS	DP=1835;AF=0.002180;SB=5;DP4=769,1067,3,1;INDEL;HRUN=4
NC_045512.2	19983	.	C	CT	137.0	PASS	DP=1533;AF=0.007828;SB=0;DP4=652,888,5,7;INDEL;HRUN=6
NC_045512.2	20091	.	C	CA	81.0	PASS	DP=1477;AF=0.003385;SB=4;DP4=814,661,4,1;INDEL;HRUN=3
NC_045512.2	20296	.	AAATT	A	64.0	PASS	DP=1333;AF=0.003001;SB=2;DP4=423,909,2,2;INDEL;HRUN=3
NC_045512.2	20890	.	G	GT	63.0	PASS	DP=1405;AF=0.002847;SB=2;DP4=957,485,2,2;INDEL;HRUN=2
NC_045512.2	21101	.	G	GT	105.0	PASS	DP=1133;AF=0.007944;SB=1;DP4=525,606,5,4;INDEL;HRUN=6
NC_045512.2	22383	.	C	CT	64.0	PASS	DP=978;AF=0.004090;SB=4;DP4=454,598,3,1;INDEL;HRUN=4
NC_045512.2	22583	.	G	GT	124.0	PASS	DP=874;AF=0.008009;SB=0;DP4=472,402,4,3;INDEL;HRUN=5
NC_045512.2	22802	.	C	CA	87.0	PASS	DP=1083;AF=0.004617;SB=1;DP4=646,483,2,3;INDEL;HRUN=3
NC_045512.2	23191	.	C	T	5808.0	PASS	DP=1605;AF=0.149533;SB=8;DP4=895,464,150,96
NC_045512.2	23568	.	GTA	G	66.0	PASS	DP=2956;AF=0.001691;SB=1;DP4=1354,1607,3,2;INDEL;HRUN=1
NC_045512.2	23621	.	G	A	76.0	PASS	DP=2968;AF=0.003032;SB=1;DP4=1090,1868,4,5
NC_045512.2	23735	.	G	GA	53.0	PASS	DP=2490;AF=0.001606;SB=0;DP4=629,1866,1,3;INDEL;HRUN=3
NC_045512.2	23835	.	G	GT	71.0	PASS	DP=1518;AF=0.003294;SB=4;DP4=924,620,2,3;INDEL;HRUN=5
NC_045512.2	24025	.	ACTT	A	76.0	PASS	DP=1327;AF=0.003768;SB=4;DP4=523,808,3,2;INDEL;HRUN=1
NC_045512.2	24358	.	C	CA	80.0	PASS	DP=1275;AF=0.003922;SB=1;DP4=861,420,3,2;INDEL;HRUN=4
NC_045512.2	24858	.	G	A	74.0	PASS	DP=1346;AF=0.005201;SB=0;DP4=511,828,3,4
NC_045512.2	24971	.	G	GT	61.0	PASS	DP=1557;AF=0.002569;SB=12;DP4=820,770,0,4;INDEL;HRUN=3
NC_045512.2	25703	.	C	CT	54.0	PASS	DP=514;AF=0.005837;SB=5;DP4=451,60,2,1;INDEL;HRUN=4
NC_045512.2	26094	.	TA	T	78.0	PASS	DP=1369;AF=0.003652;SB=2;DP4=989,383,3,2;INDEL;HRUN=4
NC_045512.2	26144	.	G	T	33850.0	PASS	DP=1012;AF=0.951581;SB=0;DP4=0,1,491,519
NC_045512.2	27175	.	C	CT	63.0	PASS	DP=1388;AF=0.002882;SB=0;DP4=537,890,1,3;INDEL;HRUN=3
NC_045512.2	27481	.	C	T	96.0	PASS	DP=1915;AF=0.005222;SB=0;DP4=1454,450,8,2
NC_045512.2	28147	.	C	CT	82.0	PASS	DP=1104;AF=0.004529;SB=1;DP4=631,491,2,3;INDEL;HRUN=4
NC_045512.2	28214	.	C	CT	307.0	PASS	DP=876;AF=0.017123;SB=3;DP4=508,368,7,8;INDEL;HRUN=5
NC_045512.2	28214	.	C	T	95.0	PASS	DP=891;AF=0.008979;SB=1;DP4=511,372,4,4
NC_045512.2	29003	.	C	A	70.0	PASS	DP=953;AF=0.006296;SB=0;DP4=401,546,2,4
NC_045512.2	29304	.	C	CA	108.0	PASS	DP=1146;AF=0.005236;SB=3;DP4=727,416,5,1;INDEL;HRUN=3
NC_045512.2	29386	.	C	T	84.0	PASS	DP=1026;AF=0.006823;SB=12;DP4=639,380,7,0
NC_045512.2	29679	.	CT	C	70.0	PASS	DP=914;AF=0.004376;SB=2;DP4=177,738,1,3;INDEL;HRUN=3