Mercurial > repos > iuc > bcftools_plugin_setgt

view test-data/view.GL.vcf @ 6:46eb13bc2c73 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit 880627162bdeb854582e9f58ddab451de35feba3
author iuc
date Tue, 12 Dec 2017 14:03:33 -0500
parents 7e1a7520e05f
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##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##reference=file:///seq/references/1000Genomes-NCBI37.fasta
##contig=<ID=11,length=135006516>
##contig=<ID=20,length=63025520>
##contig=<ID=X,length=155270560>
##contig=<ID=Y,length=59373566>
##FORMAT=<ID=GL,Number=G,Type=Float,Description="List of Phred-scaled genotype likelihoods">
##FILTER=<ID=StrandBias,Description="Min P-value for strand bias (INFO/PV4) [0.0001]">
##FILTER=<ID=BaseQualBias,Description="Min P-value for baseQ bias (INFO/PV4) [1e-100]">
##FILTER=<ID=MapQualBias,Description="Min P-value for mapQ bias (INFO/PV4) [0]">
##FILTER=<ID=EndDistBias,Description="Min P-value for end distance bias (INFO/PV4) [0.0001]">
##FILTER=<ID=MinAB,Description="Minimum number of alternate bases (INFO/DP4) [2]">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NA00001	NA00002	NA00003
11	2343543	.	A	.	999	PASS	.	GL	0,-25.5,-25.5	0,-25.5,-25.5	0,-25.5,-25.5
11	5464562	.	C	T	999	PASS	.	GL	0,0,0	0,0,0	0,0,0
20	76962	rs6111385	T	C	999	PASS	.	GL	-25.5,0,-25.5	-25.5,-25.5,0	-25.5,-25.5,0
20	126310	.	ACC	A	999	StrandBias;EndDistBias	.	GL	-25.5,0,-13.2	-25.5,0,-13.9	-25.5,-21.3,0
20	138125	rs2298108	G	T	999	PASS	.	GL	-13.5,0,-16.3	-14,0,-25.5	-25.5,-19.9,0
20	138148	rs2298109	C	T	999	PASS	.	GL	-19.5,0,-25.5	-19.2,0,-25.5	-25.5,-23.5,0
20	271225	.	T	TTTA,TA	999	StrandBias	.	GL	-15.1,-5.3,-20.3,0,-5.2,-15.9	-25.5,0,-21.3,-25.5,-25.5,-25.5	-25.5,-25.5,-25.5,-25.5,0,-24.1
20	304568	.	C	T	999	PASS	.	GL	-9.5,0,-25.5	-19.2,0,-25.5	-25.5,-9.5,0
20	326891	.	A	AC	999	PASS	.	GL	-25.5,0,-13.2	-25.5,0,-13.9	.,.,.
X	2928329	rs62584840	C	T	999	PASS	.	GL	0,-5.6	0,-8.1	-7.3,0,-1.9
X	2933066	rs61746890	G	C	999	PASS	.	GL	0,-25.5	0,-25.5	-25.5,-25.5,-25.5
X	2942109	rs5939407	T	C	999	PASS	.	GL	0,-25.5	-25.5,0	-25.5,-15.7,0
X	3048719	.	T	C	999	PASS	.	GL	0,-25.5	-25.5,0	-25.5,0,-15.7
Y	8657215	.	C	A	999	PASS	.	GL	0,-25.5	-25.5,0	.
Y	10011673	rs78249411	G	A	999	MinAB	.	GL	-12.6,-10.1	-9.5,0	.