annotate test-results/Variant_Non-coding.Result.tsv @ 0:83181dabeb90 draft

planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatool commit 4f73619e5f750916a9971e433ddd6b8dee0d7dd3

#Non-coding Variant Report
#2018-05-18 15:18:04.020642
#CRAVAT version: hybrid
#Analysis done at http://www.cravat.us.
#Job Id: znylund_20180518_111800
#Input file: _VCF_BEDintersect_on_data_65_and_data_6_.vcf
#This report shows analysis results at variant level.
#hg38 genomic.
#N/A
#For more information on CRAVAT, visit http://www.cravat.us.

Input line	ID	Chromosome	Position	Strand	Reference base(s)	Alternate base(s)	Sample ID	HUGO symbol	Sequence ontology	Protein sequence change	ClinVar	COSMIC ID	COSMIC variant count (tissue)	Number of samples with variant	dbSNP	ESP6500 AF (average)	gnomAD AF Total	gnomAD AF African	gnomAD AF American	gnomAD AF Ashkenazi Jewish	gnomAD AF East Asian	gnomAD AF Finnish	gnomAD AF Non-Finnish European	gnomAD AF Other	gnomAD AF South Asian	GWAS NHLBI Key (GRASP)	GWAS PMID (GRASP)	GWAS Phenotype (GRASP)	Protein 3D variant	In TCGA Mutation Cluster	ncRNA Class	ncRNA Name	Pseudogene	Pseudogene Transcript	Repeat Class	Repeat Family	Repeat Name	TARGET	1000 Genomes AF	UTR/Intron	UTR/Intron Gene	UTR/Intron All Transcript	Phred	VCF filters	Zygosity	Alternate reads	Total reads	Variant allele frequency	VEST p-value	VEST FDR	CGL driver class
8	VAR524_unknown	chr19	17205444	+	T	C	unknown	Non-Coding						1	rs2305763	0.0	0.510502431118	0.684095610205	0.693317422434	0.337748344371	0.795930949445	0.435243553009	0.393043827905	0.449691991786															0.629792	intron	MYO9B	ENST00000595618.5(intron),ENST00000594824.5(intron),ENST00000397274.6(intron)	206.198	.	hom	14	7	2.0