view test-results/Variant_Result.tsv @ 0:83181dabeb90 draft

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

#Variant Report
#2018-05-18 15:15:25.119179
#CRAVAT version: hybrid
#Analysis done at http://www.cravat.us.
#Job Id: znylund_20180518_111521
#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
1	VAR516_unknown	chr1	156705422	+	T	C	unknown	CRABP2	MS	K9E		COSM1984142	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr1:156705422										0				125181	.	het	5739	18018	0.318514818515	0.53061		
2	VAR517_unknown	chr12	6561055	+	T	C	unknown	NOP2	MS	N408S				1		0.0													../MuPIT_Interactive?gm=chr12:6561055										0				14340.8	.	het	910	3868	0.235263702172	0.00324		
3	VAR518_unknown	chr12	110339630	+	C	T	unknown	ATP2A2	MS	T557I				1		0.0													../MuPIT_Interactive?gm=chr12:110339630										0				48828.1	.	het	2447	9100	0.268901098901	0.00374		
4	VAR520_unknown	chr14	102011985	+	A	T	unknown	DYNC1H1	MS	R2243S		COSM2262213	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr14:102011985										0				12962.3	.	het	642	2131	0.301267010793	0.02307		
5	VAR521_unknown	chr14	102083954	+	C	T	unknown	HSP90AA1	MS	D515N		COSM2262393	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr14:102083954										0				240809	.	het	17374	85275	0.203740838464	0.02014		
6	VAR522_unknown	chr17	82082606	+	C	T	unknown	FASN	MS	S1947N		COSM4648107	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr17:82082606										0				10374.8	.	het	776	3826	0.202822791427	0.18611		
7	VAR523_unknown	chr19	17205335	+	A	T	unknown	MYO9B	MS	K1688M				1		0.0													../MuPIT_Interactive?gm=chr19:17205335										0				0.00158993	.	het	2	7	0.285714285714	0.20028		
9	VAR525_unknown	chr19	17205973	+	T	C	unknown	MYO9B	MS	V1693A		COSM438878	thyroid(2)	1	rs7248508	0.522744	0.526958747465	0.685404424473	0.728029336735	0.352247807018	0.776672496721	0.453231381586	0.406255640183	0.486462728551	0.596900776808	190609063506732,203395363506733,206865653506734,208819603506735,224846277709335,224792027709336	19060906,20339536,20686565,20881960,22484627,22479202	LDL cholesterol(0.0152),HDL cholesterol(0.0279),Triglycerides(0.0141),Height(0.0104),Obesity with early age of onset (age >2)(0.0471),Adiponectin levels(0.0294)	../MuPIT_Interactive?gm=chr19:17205973										0.631589				12243.8	.	hom	812	406	2.0	0.95254		
10	VAR526_unknown	chr19	18856059	+	C	T	unknown	UPF1	MS	A571V		COSM3100527	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr19:18856059										0				10269.5	.	het	592	2379	0.248844052123	0.09372