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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/freyja commit 79a21a9a4a63e538f2ba0bc29384593df2c65859
author iuc
date Fri, 15 Nov 2024 16:44:42 +0000
parents 0ceb9fb0f4ce
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##fileformat=VCFv4.0
##fileDate=20220125
##source=lofreq call -f freyja/data/NC_045512_Hu-1.fasta -o test.vcf freyja/data/test.bam 
##reference=freyja/data/NC_045512_Hu-1.fasta
##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_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_64,Description="Minimum SNV Quality (Phred) 64">
##FILTER=<ID=min_indelqual_20,Description="Minimum Indel Quality (Phred) 20">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
NC_045512.2	210	.	G	T	48519	PASS	DP=3206;AF=0.500312;SB=13;DP4=585,1012,533,1071
NC_045512.2	241	.	C	T	49314	PASS	DP=3610;AF=0.497230;SB=9;DP4=580,1229,530,1265
NC_045512.2	372	.	A	C	110	PASS	DP=1369;AF=0.008766;SB=1;DP4=568,789,4,8
NC_045512.2	441	.	G	A	105	PASS	DP=2250;AF=0.007111;SB=2;DP4=893,1338,5,11
NC_045512.2	1055	.	G	A	1592	PASS	DP=300;AF=0.220000;SB=1;DP4=127,106,34,32
NC_045512.2	1191	.	C	T	11391	PASS	DP=850;AF=0.450588;SB=1;DP4=215,252,181,202
NC_045512.2	1267	.	C	T	9741	PASS	DP=577;AF=0.549393;SB=1;DP4=144,116,170,147
NC_045512.2	2184	.	A	C	154	PASS	DP=888;AF=0.014640;SB=1;DP4=768,107,11,2
NC_045512.2	2973	.	C	T	1395	PASS	DP=1368;AF=0.057749;SB=20;DP4=862,427,41,38
NC_045512.2	3037	.	C	T	13537	PASS	DP=1209;AF=0.401158;SB=0;DP4=209,511,139,346
NC_045512.2	4897	.	C	T	159	PASS	DP=431;AF=0.027842;SB=1;DP4=235,184,6,6
NC_045512.2	5184	.	C	T	3943	PASS	DP=347;AF=0.409222;SB=1;DP4=197,8,135,7
NC_045512.2	5457	.	C	T	949	PASS	DP=1254;AF=0.044657;SB=1;DP4=722,476,35,21
NC_045512.2	6996	.	T	C	80	PASS	DP=98;AF=0.040816;SB=0;DP4=48,46,2,2
NC_045512.2	8782	.	C	T	32957	PASS	DP=1458;AF=0.693416;SB=8;DP4=170,277,344,667
NC_045512.2	8883	.	T	C	72	PASS	DP=506;AF=0.015810;SB=6;DP4=113,384,0,8
NC_045512.2	9203	.	G	A	10829	PASS	DP=1088;AF=0.351103;SB=8;DP4=307,398,185,197
NC_045512.2	9678	.	T	C	1593	PASS	DP=109;AF=0.486239;SB=5;DP4=11,45,16,37
NC_045512.2	11005	.	C	A	4808	PASS	DP=467;AF=0.368308;SB=0;DP4=191,103,112,60
NC_045512.2	11414	.	C	T	246	PASS	DP=529;AF=0.030246;SB=6;DP4=398,115,10,6
NC_045512.2	12235	.	A	C	117	PASS	DP=603;AF=0.018242;SB=5;DP4=60,532,2,9
NC_045512.2	12583	.	T	A	67	PASS	DP=1093;AF=0.006404;SB=0;DP4=588,498,4,3
NC_045512.2	14256	.	A	C	75	PASS	DP=1404;AF=0.010684;SB=0;DP4=689,697,7,8
NC_045512.2	14408	.	C	T	1357	PASS	DP=108;AF=0.472222;SB=2;DP4=18,39,19,32
NC_045512.2	16247	.	C	T	99	PASS	DP=462;AF=0.021645;SB=2;DP4=283,169,5,5
NC_045512.2	16255	.	C	T	77	PASS	DP=464;AF=0.012931;SB=1;DP4=285,173,3,3
NC_045512.2	17000	.	C	T	115	PASS	DP=1044;AF=0.010536;SB=0;DP4=501,532,5,6
NC_045512.2	17474	.	C	A	106	PASS	DP=758;AF=0.015831;SB=1;DP4=405,341,6,6
NC_045512.2	17496	.	A	G	6152	PASS	DP=504;AF=0.430556;SB=0;DP4=88,199,67,150
NC_045512.2	18060	.	C	T	14317	PASS	DP=767;AF=0.598435;SB=2;DP4=24,284,41,418
NC_045512.2	18096	.	T	C	125	PASS	DP=161;AF=0.043478;SB=1;DP4=59,95,2,5
NC_045512.2	18311	.	T	C	121	PASS	DP=869;AF=0.011507;SB=16;DP4=432,427,1,9
NC_045512.2	18395	.	C	T	82	PASS	DP=1038;AF=0.009634;SB=1;DP4=568,456,5,5
NC_045512.2	19547	.	C	T	851	PASS	DP=863;AF=0.054461;SB=0;DP4=409,407,24,23
NC_045512.2	20396	.	A	G	489	PASS	DP=32;AF=0.500000;SB=0;DP4=14,2,14,2
NC_045512.2	21618	.	C	G	375	PASS	DP=40;AF=0.375000;SB=1;DP4=15,9,11,4
NC_045512.2	21792	.	A	C	4658	PASS	DP=477;AF=0.354298;SB=0;DP4=154,154,83,86
NC_045512.2	21849	.	A	C	75	PASS	DP=288;AF=0.017361;SB=2;DP4=41,239,1,4
NC_045512.2	21974	.	G	T	82	PASS	DP=168;AF=0.029762;SB=0;DP4=59,104,2,3
NC_045512.2	21987	.	G	A	4045	PASS	DP=333;AF=0.420420;SB=0;DP4=93,100,68,72
NC_045512.2	22009	.	C	A	330	PASS	DP=333;AF=0.060060;SB=0;DP4=151,162,10,10
NC_045512.2	22206	.	A	G	1045	PASS	DP=341;AF=0.131965;SB=0;DP4=142,153,21,24
NC_045512.2	22296	.	A	G	103	PASS	DP=518;AF=0.015444;SB=3;DP4=340,167,4,4
NC_045512.2	22482	.	C	T	79	PASS	DP=158;AF=0.031646;SB=0;DP4=51,102,2,3
NC_045512.2	22995	.	C	A	3384	PASS	DP=222;AF=0.504505;SB=0;DP4=60,50,61,51
NC_045512.2	23403	.	A	G	6370	PASS	DP=556;AF=0.395683;SB=10;DP4=166,169,126,94
NC_045512.2	23525	.	C	T	125	PASS	DP=358;AF=0.025140;SB=0;DP4=67,282,1,8
NC_045512.2	23601	.	C	T	66	PASS	DP=957;AF=0.009404;SB=1;DP4=427,520,5,4
NC_045512.2	23604	.	C	G	13373	PASS	DP=959;AF=0.488008;SB=0;DP4=220,271,211,257
NC_045512.2	23607	.	G	T	532	PASS	DP=958;AF=0.037578;SB=0;DP4=412,506,17,19
NC_045512.2	23618	.	A	G	83	PASS	DP=959;AF=0.011470;SB=0;DP4=424,524,5,6
NC_045512.2	24410	.	G	A	267	PASS	DP=22;AF=0.409091;SB=0;DP4=4,9,3,6
NC_045512.2	24780	.	A	G	84	PASS	DP=707;AF=0.012730;SB=2;DP4=316,382,3,6
NC_045512.2	25469	.	C	T	10803	PASS	DP=1085;AF=0.355760;SB=1;DP4=210,488,111,275
NC_045512.2	25606	.	G	A	64	PASS	DP=2215;AF=0.005418;SB=0;DP4=1181,1016,6,6
NC_045512.2	26542	.	C	T	362	PASS	DP=78;AF=0.179487;SB=6;DP4=41,23,6,8
NC_045512.2	26767	.	T	C	5916	PASS	DP=531;AF=0.384181;SB=3;DP4=219,108,130,74
NC_045512.2	27752	.	C	T	2820	PASS	DP=415;AF=0.260241;SB=18;DP4=184,123,79,29
NC_045512.2	27920	.	C	T	167	PASS	DP=2351;AF=0.008932;SB=0;DP4=1543,786,14,7
NC_045512.2	27924	.	A	C	1081	PASS	DP=2351;AF=0.030200;SB=0;DP4=1511,768,46,25
NC_045512.2	28144	.	T	C	17994	PASS	DP=669;AF=0.792227;SB=22;DP4=45,94,243,287
NC_045512.2	28253	.	C	T	5868	PASS	DP=471;AF=0.430998;SB=217;DP4=15,251,86,117
NC_045512.2	28387	.	A	C	109	PASS	DP=1287;AF=0.012432;SB=6;DP4=1141,129,13,3
NC_045512.2	28461	.	A	G	29706	PASS	DP=2257;AF=0.443952;SB=1;DP4=688,565,540,462
NC_045512.2	28698	.	C	A	7287	PASS	DP=544;AF=0.455882;SB=0;DP4=180,114,151,97
NC_045512.2	28836	.	C	T	102	PASS	DP=815;AF=0.011043;SB=0;DP4=495,310,6,3
NC_045512.2	28851	.	G	T	72	PASS	DP=815;AF=0.009816;SB=3;DP4=497,310,4,4
NC_045512.2	28853	.	T	A	2280	PASS	DP=817;AF=0.124847;SB=3;DP4=441,273,59,43
NC_045512.2	28881	.	G	T	9326	PASS	DP=721;AF=0.443828;SB=2;DP4=221,180,183,137
NC_045512.2	29402	.	G	T	30263	PASS	DP=1934;AF=0.512410;SB=45;DP4=700,243,814,177
NC_045512.2	29512	.	T	C	44232	PASS	DP=2655;AF=0.554802;SB=7;DP4=670,511,797,676
NC_045512.2	29581	.	T	C	227	PASS	DP=2170;AF=0.011982;SB=0;DP4=1905,221,24,2
NC_045512.2	29742	.	G	T	1184	PASS	DP=60;AF=0.616667;SB=0;DP4=7,16,11,26