Mercurial > repos > iuc > fermikit_variants

view test-data/flt.vcf @ 1:ed056d243455 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/fermikit commit ab4afb50e6c991cc2e784a93a0c7a75329eac88c
author iuc
date Mon, 27 Jun 2022 11:22:33 +0000
parents 44519e762f16
children
line wrap: on
line source

##fileformat=VCFv4.1
##source=htsbox-pileup-r327
##reference=/tmp/tmpIcvwsb/files/000/dataset_2.dat
##contig=<ID=11_1910000_1940000,length=30001>
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=AD,Number=R,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##INFO=<ID=_DP,Number=1,Type=Integer,Description="Raw read depth">
##INFO=<ID=_DS,Number=1,Type=Integer,Description="min{alt_DP_on_forward, alt_DP_on_reverse}">
##INFO=<ID=_AB,Number=1,Type=Integer,Description="Percentage of non-reference reads">
##INFO=<ID=_FS,Number=1,Type=Integer,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##FILTER=<ID=DPhigh,Description="High read depth: _DP>62.82">
##FILTER=<ID=DPlow,Description="Low read depth: _DP<3">
##FILTER=<ID=FShigh,Description="Large Fisher-Strand bias: _FS>30">
##FILTER=<ID=ABlow,Description="Low fraction of non-reference reads: _AB<30 at SNPs or _AB<30 at INDELs">
##FILTER=<ID=DSlow,Description="Low double-strand support at SNPs: _DS<1">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	aligned_contigs_bam
11_1910000_1940000	636	.	c	T	25	.	_DP=39;_AB=64	GT:AD	1/0:14,25
11_1910000_1940000	708	.	t	C	40	.	_DP=40;_AB=100	GT:AD	1/1:0,40
11_1910000_1940000	1116	.	t	C	43	.	_DP=43;_AB=100	GT:AD	1/1:0,43
11_1910000_1940000	1891	.	t	C	44	.	_DP=44;_AB=100	GT:AD	1/1:0,44
11_1910000_1940000	2297	.	a	G	43	.	_DP=43;_AB=100	GT:AD	1/1:0,43
11_1910000_1940000	2727	.	a	G	42	.	_DP=42;_AB=100	GT:AD	1/1:0,42
11_1910000_1940000	3378	.	a	G	50	.	_DP=50;_AB=100	GT:AD	1/1:0,50
11_1910000_1940000	4140	.	c	T	21	.	_DP=36;_AB=58	GT:AD	1/0:15,21
11_1910000_1940000	4820	.	g	A	35	.	_DP=35;_AB=100	GT:AD	1/1:0,35
11_1910000_1940000	4860	.	t	G	36	.	_DP=36;_AB=100	GT:AD	1/1:0,36
11_1910000_1940000	4976	.	g	A	33	.	_DP=33;_AB=100	GT:AD	1/1:0,33
11_1910000_1940000	5455	.	a	AGT	12	.	_DP=25;_AB=48	GT:AD	0/1:13,12
11_1910000_1940000	5559	.	g	T	39	.	_DP=39;_AB=100	GT:AD	1/1:0,39
11_1910000_1940000	6369	.	ct	C	8	ABlow	_DP=42;_AB=19	GT:AD	0/1:34,8
11_1910000_1940000	6654	.	g	A	43	.	_DP=43;_AB=100	GT:AD	1/1:0,43
11_1910000_1940000	7873	.	g	A	45	.	_DP=45;_AB=100	GT:AD	1/1:0,45
11_1910000_1940000	8084	.	t	C	54	.	_DP=54;_AB=100	GT:AD	1/1:0,54
11_1910000_1940000	10894	.	t	G	40	.	_DP=40;_AB=100	GT:AD	1/1:0,40
11_1910000_1940000	12259	.	a	G	35	.	_DP=35;_AB=100	GT:AD	1/1:0,35
11_1910000_1940000	15695	.	g	A	36	.	_DP=36;_AB=100	GT:AD	1/1:0,36
11_1910000_1940000	16353	.	ctt	C	14	.	_DP=14;_AB=100	GT:AD	1/1:0,14
11_1910000_1940000	20714	.	c	T	24	.	_DP=42;_AB=57	GT:AD	1/0:18,24
11_1910000_1940000	24531	.	t	G	32	.	_DP=32;_AB=100	GT:AD	1/1:0,32
11_1910000_1940000	24546	.	gt	G	25	.	_DP=25;_AB=100	GT:AD	1/1:0,25
11_1910000_1940000	25710	.	t	TTG	17	.	_DP=46;_AB=37	GT:AD	0/1:29,17
11_1910000_1940000	25813	.	c	CTG,CTGTG	13	.	_DP=33;_AB=70	GT:AD	1/0:10,13,10
11_1910000_1940000	26084	.	ctg	C,CTGTGTG	17	.	_DP=36;_AB=75	GT:AD	1/2:9,17,10
11_1910000_1940000	26212	.	g	A	29	.	_DP=55;_AB=53	GT:AD	1/0:26,29
11_1910000_1940000	26370	.	c	CTG,CTGTGTG	12	.	_DP=34;_AB=68	GT:AD	1/0:11,12,11
11_1910000_1940000	26521	.	a	G	30	.	_DP=30;_AB=100	GT:AD	1/1:0,30
11_1910000_1940000	26713	.	a	G	32	.	_DP=32;_AB=100	GT:AD	1/1:0,32
11_1910000_1940000	27735	.	tc	T	41	.	_DP=41;_AB=100	GT:AD	1/1:0,41
11_1910000_1940000	28524	.	c	A	18	.	_DP=38;_AB=47	GT:AD	0/1:20,18