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view test-data/hg19/test1.vcf @ 2:2cba79e6037e draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/bumbershoot/custom_pro_db commit 9910ed076e4b8a3f083351b89fa861d0a4a93beb
author galaxyp
date Wed, 17 May 2017 20:23:39 -0400
parents ad130eaa3a05
children
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##fileformat=VCFv4.1
##samtoolsVersion=0.1.17 (r973:277)
##INFO=<ID=DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=DP4,Number=4,Type=Integer,Description="# high-quality ref-forward bases, ref-reverse, alt-forward and alt-reverse bases">
##INFO=<ID=MQ,Number=1,Type=Integer,Description="Root-mean-square mapping quality of covering reads">
##INFO=<ID=FQ,Number=1,Type=Float,Description="Phred probability of all samples being the same">
##INFO=<ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele frequency (assuming HWE)">
##INFO=<ID=AC1,Number=1,Type=Float,Description="Max-likelihood estimate of the first ALT allele count (no HWE assumption)">
##INFO=<ID=G3,Number=3,Type=Float,Description="ML estimate of genotype frequencies">
##INFO=<ID=HWE,Number=1,Type=Float,Description="Chi^2 based HWE test P-value based on G3">
##INFO=<ID=CLR,Number=1,Type=Integer,Description="Log ratio of genotype likelihoods with and without the constraint">
##INFO=<ID=UGT,Number=1,Type=String,Description="The most probable unconstrained genotype configuration in the trio">
##INFO=<ID=CGT,Number=1,Type=String,Description="The most probable constrained genotype configuration in the trio">
##INFO=<ID=PV4,Number=4,Type=Float,Description="P-values for strand bias, baseQ bias, mapQ bias and tail distance bias">
##INFO=<ID=INDEL,Number=0,Type=Flag,Description="Indicates that the variant is an INDEL.">
##INFO=<ID=PC2,Number=2,Type=Integer,Description="Phred probability of the nonRef allele frequency in group1 samples being larger (,smaller) than in group2.">
##INFO=<ID=PCHI2,Number=1,Type=Float,Description="Posterior weighted chi^2 P-value for testing the association between group1 and group2 samples.">
##INFO=<ID=QCHI2,Number=1,Type=Integer,Description="Phred scaled PCHI2.">
##INFO=<ID=PR,Number=1,Type=Integer,Description="# permutations yielding a smaller PCHI2.">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GL,Number=3,Type=Float,Description="Likelihoods for RR,RA,AA genotypes (R=ref,A=alt)">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="# high-quality bases">
##FORMAT=<ID=SP,Number=1,Type=Integer,Description="Phred-scaled strand bias P-value">
##FORMAT=<ID=PL,Number=-1,Type=Integer,Description="List of Phred-scaled genotype likelihoods, number of values is (#ALT+1)*(#ALT+2)/2">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	test
chr1	32386425	.	T	C	24	.	DP=3;AF1=1;AC1=2;DP4=0,0,0,3;MQ=50;FQ=-36	GT:PL:GQ	1/1:56,9,0:15
chr1	32507666	.	G	T	6.2	.	DP=5;AF1=0.4999;AC1=1;DP4=3,0,2,0;MQ=50;FQ=8.65;PV4=1,0.062,1,0.36	GT:PL:GQ	0/1:35,0,78:36
chr1	32524459	.	A	C	3.54	.	DP=5;AF1=0.4998;AC1=1;DP4=1,2,0,2;MQ=50;FQ=5.47;PV4=1,0.0021,1,1	GT:PL:GQ	0/1:31,0,98:30
chr1	32622505	.	G	A	101	.	DP=18;AF1=0.5;AC1=1;DP4=10,0,5,2;MQ=50;FQ=104;PV4=0.15,0.0055,1,0.0075	GT:PL:GQ	0/1:131,0,162:99
chr12	25357574	.	CAA	C	109	.	INDEL;DP=5;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-46.5	GT:PL:GQ	1/1:149,12,0:21
chr12	25357628	.	TA	T	53.4	.	INDEL;DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-43.5	GT:PL:GQ	1/1:93,9,0:16
chr12	25358650	.	A	T	73	.	DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-72	GT:PL:GQ	1/1:106,45,0:87
chr12	25358662	.	CTTTTTTTT	CTTTTTT,CTTTTTTT	31.6	.	INDEL;DP=38;AF1=1;AC1=2;DP4=0,0,15,0;MQ=50;FQ=-52.5	GT:PL:GQ	1/1:96,42,24,91,0,64:33
chr12	25358943	.	T	C	67.1	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:100,21,0:39
chr12	25358969	.	T	G	36.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:69,12,0:21
chr12	25359352	.	G	A	172	.	DP=16;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:205,42,0:81
chr12	25359464	.	TAA	TA	123	.	INDEL;DP=26;AF1=1;AC1=2;DP4=0,0,26,0;MQ=50;FQ=-113	GT:PL:GQ	1/1:164,78,0:99
chr12	25360138	.	T	C	169	.	DP=21;AF1=1;AC1=2;DP4=0,0,19,0;MQ=50;FQ=-84	GT:PL:GQ	1/1:202,57,0:99
chr12	25361091	.	T	C	93	.	DP=15;AF1=1;AC1=2;DP4=0,0,14,0;MQ=50;FQ=-69	GT:PL:GQ	1/1:126,42,0:81
chr12	25362217	.	A	G	179	.	DP=20;AF1=1;AC1=2;DP4=0,0,20,0;MQ=50;FQ=-87	GT:PL:GQ	1/1:212,60,0:99
chr12	25362465	.	G	A	38.3	.	DP=18;AF1=1;AC1=2;DP4=0,0,5,0;MQ=50;FQ=-42	GT:PL:GQ	1/1:71,15,0:27
chr12	25362552	.	A	C	156	.	DP=10;AF1=1;AC1=2;DP4=0,0,10,0;MQ=50;FQ=-57	GT:PL:GQ	1/1:189,30,0:57
chr12	25364387	.	T	C	21	.	DP=7;AF1=0.5;AC1=1;DP4=3,1,0,2;MQ=50;FQ=24;PV4=0.4,1,1,1	GT:PL:GQ	0/1:51,0,112:54
chr12	25368462	.	C	T	112	.	DP=7;AF1=1;AC1=2;DP4=0,0,7,0;MQ=50;FQ=-48	GT:PL:GQ	1/1:145,21,0:39
chr17	37866082	.	G	A	141	.	DP=45;AF1=0.5;AC1=1;DP4=25,0,20,0;MQ=50;FQ=144;PV4=1,1,1,1	GT:PL:GQ	0/1:171,0,180:99
chr17	37870047	.	A	G	30	.	DP=3;AF1=0.5008;AC1=1;DP4=0,1,2,0;MQ=50;FQ=-4.12;PV4=0.33,1,1,1	GT:PL:GQ	0/1:60,0,25:28
chr17	37879466	.	G	A	7.8	.	DP=3;AF1=0.5001;AC1=1;DP4=1,0,1,1;MQ=50;FQ=4.79;PV4=1,0.064,1,1	GT:PL:GQ	0/1:37,0,31:34
chr17	37885332	.	G	A	83.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,0,4;MQ=50;FQ=-39	GT:PL:GQ	1/1:116,12,0:21
chr17	37898543	.	T	C	165	.	DP=26;AF1=1;AC1=2;DP4=0,0,21,0;MQ=50;FQ=-90	GT:PL:GQ	1/1:198,63,0:99
chr17	7530271	.	C	T	143	.	DP=71;AF1=0.5;AC1=1;DP4=32,2,34,0;MQ=50;FQ=146;PV4=0.49,4.1e-06,1,1	GT:PL:GQ	0/1:173,0,238:99
chr17	7572657	.	G	T	225	.	DP=122;AF1=0.5;AC1=1;DP4=59,0,58,3;MQ=50;FQ=163;PV4=0.24,0.06,1,0.27	GT:PL:GQ	0/1:255,0,190:99
chr17	7591866	.	G	T	45	.	DP=14;AF1=0.5;AC1=1;DP4=10,0,4,0;MQ=50;FQ=48;PV4=1,0.062,1,0.01	GT:PL:GQ	0/1:75,0,162:78
chr17	7606153	.	C	T	74	.	DP=16;AF1=0.5;AC1=1;DP4=10,0,5,0;MQ=50;FQ=77;PV4=1,0.12,1,1	GT:PL:GQ	0/1:104,0,165:99
chr2	48010558	.	C	A	12.3	.	DP=7;AF1=0.5002;AC1=1;DP4=1,0,2,0;MQ=50;FQ=5.23;PV4=1,0.065,1,1	GT:PL:GQ	0/1:42,0,31:34
chr2	48016554	.	T	C	32	.	DP=4;AF1=0.5;AC1=1;DP4=1,1,2,0;MQ=50;FQ=20.9;PV4=1,1,1,0.21	GT:PL:GQ	0/1:62,0,48:51
chr2	48018081	.	A	G	77	.	DP=6;AF1=0.501;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-4.75;PV4=1,1,1,0.34	GT:PL:GQ	0/1:107,0,24:27
chr2	48018221	.	C	T	22	.	DP=7;AF1=0.5;AC1=1;DP4=5,0,2,0;MQ=50;FQ=25;PV4=1,1,1,1	GT:PL:GQ	0/1:52,0,116:55
chr2	48027990	.	G	T	122	.	DP=17;AF1=0.5;AC1=1;DP4=7,0,9,0;MQ=50;FQ=104;PV4=1,1,1,0.039	GT:PL:GQ	0/1:152,0,131:99
chr2	48030458	.	G	C	105	.	DP=4;AF1=1;AC1=2;DP4=0,0,3,1;MQ=50;FQ=-39	GT:PL:GQ	1/1:137,12,0:21
chr5	112154737	.	CT	C	29	.	INDEL;DP=5;AF1=0.5;AC1=1;DP4=3,0,2,0;MQ=50;FQ=32;PV4=1,1,1,0.0012	GT:PL:GQ	0/1:59,0,85:62
chr5	112162854	.	T	C	60	.	DP=3;AF1=1;AC1=2;DP4=0,0,3,0;MQ=50;FQ=-36	GT:PL:GQ	1/1:92,9,0:16
chr5	112164561	.	G	A	87.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:120,12,0:21
chr5	112175639	.	C	T	31	.	DP=4;AF1=0.5;AC1=1;DP4=2,0,2,0;MQ=50;FQ=31.5;PV4=1,0.21,1,1	GT:PL:GQ	0/1:61,0,62:61
chr5	112175897	.	GAA	GA	7.8	.	INDEL;DP=7;AF1=0.5;AC1=1;DP4=4,0,3,0;MQ=50;FQ=10.4;PV4=1,0.0018,1,0.33	GT:PL:GQ	0/1:37,0,97:39
chr5	112176559	.	T	G	72	.	DP=11;AF1=1;AC1=2;DP4=0,0,8,0;MQ=50;FQ=-51	GT:PL:GQ	1/1:105,24,0:45
chr5	112176756	.	T	A	143	.	DP=10;AF1=1;AC1=2;DP4=0,0,9,0;MQ=50;FQ=-54	GT:PL:GQ	1/1:176,27,0:51
chr5	112180015	.	C	A	123	.	DP=11;AF1=0.5;AC1=1;DP4=3,0,8,0;MQ=50;FQ=40;PV4=1,1,1,1	GT:PL:GQ	0/1:153,0,67:70
chr5	112204170	.	G	A	112	.	DP=5;AF1=1;AC1=2;DP4=0,0,2,2;MQ=50;FQ=-39	GT:PL:GQ	1/1:144,12,0:21
chr7	140043303	.	C	T	88	.	DP=18;AF1=0.5;AC1=1;DP4=11,0,7,0;MQ=50;FQ=91;PV4=1,0.00034,1,0.42	GT:PL:GQ	0/1:118,0,167:99
chr7	140065806	.	T	C	38.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:71,12,0:21
chr7	140065845	.	C	A	44.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:77,12,0:21
chr7	140152904	.	CAAAA	CAAAAA	41.5	.	INDEL;DP=42;AF1=0.5;AC1=1;DP4=23,0,16,0;MQ=50;FQ=44.2;PV4=1,1,1,1	GT:PL:GQ	0/1:79,0,91:82
chr7	140153495	.	G	T	140	.	DP=52;AF1=0.5;AC1=1;DP4=28,0,22,0;MQ=50;FQ=143;PV4=1,0.082,1,0.00038	GT:PL:GQ	0/1:170,0,184:99
chr7	140158851	.	C	G	153	.	DP=36;AF1=1;AC1=2;DP4=1,0,33,0;MQ=50;FQ=-102;PV4=1,1,1,1	GT:PL:GQ	1/1:186,75,0:99
chr7	140244560	.	C	T	78	.	DP=6;AF1=0.5013;AC1=1;DP4=1,0,4,0;MQ=50;FQ=-5.45;PV4=1,1,1,1	GT:PL:GQ	0/1:108,0,23:26
chr7	140406430	.	T	A	8.64	.	DP=27;AF1=0.5;AC1=1;DP4=19,0,6,0;MQ=50;FQ=11.3;PV4=1,1,1,0.00021	GT:PL:GQ	0/1:38,0,167:40
chr7	140406436	.	A	G	4.77	.	DP=14;AF1=0.4999;AC1=1;DP4=12,0,2,0;MQ=50;FQ=6.99;PV4=1,1,1,0.08	GT:PL:GQ	0/1:33,0,170:33
chr7	140424582	.	G	C	18.1	.	DP=5;AF1=0.5;AC1=1;DP4=0,2,1,2;MQ=50;FQ=20.4;PV4=1,0.00086,1,1	GT:PL:GQ	0/1:48,0,56:50
chr7	140426098	.	G	A	10.2	.	DP=3;AF1=1;AC1=2;DP4=0,0,2,0;MQ=50;FQ=-33	GT:PL:GQ	1/1:41,6,0:8
chr7	140702871	.	G	A	77.5	.	DP=4;AF1=1;AC1=2;DP4=0,0,4,0;MQ=50;FQ=-39	GT:PL:GQ	1/1:110,12,0:21
chr7	140706061	.	G	T	119	.	DP=74;AF1=0.5;AC1=1;DP4=45,0,22,0;MQ=50;FQ=122;PV4=1,1,1,1	GT:PL:GQ	0/1:149,0,178:99
chr7	140706157	.	G	T	42	.	DP=25;AF1=0.5;AC1=1;DP4=13,0,9,0;MQ=50;FQ=45;PV4=1,5.7e-11,1,0.013	GT:PL:GQ	0/1:72,0,170:75
chr9	86583076	.	C	T	64	.	DP=17;AF1=0.5;AC1=1;DP4=5,0,11,0;MQ=50;FQ=66;PV4=1,1.4e-08,1,1	GT:PL:GQ	0/1:94,0,100:96
chr9	86593314	.	G	C	186	.	DP=203;AF1=0.5;AC1=1;DP4=100,0,99,0;MQ=50;FQ=186;PV4=1,1,1,0.072	GT:PL:GQ	0/1:216,0,216:99
chr9	86595070	.	C	T	140	.	DP=93;AF1=0.5;AC1=1;DP4=53,0,38,0;MQ=50;FQ=143;PV4=1,0.43,1,1	GT:PL:GQ	0/1:170,0,188:99
chr9	86595498	.	G	A	66	.	DP=128;AF1=0.5;AC1=1;DP4=50,2,76,0;MQ=50;FQ=69;PV4=0.16,6e-81,1,1	GT:PL:GQ	0/1:96,0,225:99