annotate test-data/variant.tsv @ 1:2c7bcc1219fc draft

Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.

#Variant Report
#2018-08-13 15:36:32.354483
#CRAVAT version: hybrid
#Analysis done at http://www.cravat.us.
#Job Id: rsajulga_20180813_113614
#Input file: Freebayes_two_variants.vcf
#This report shows analysis results at variant level.
#hg38 genomic.
#Breast
#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	Reference peptide	Variant peptide	CHASM p-value	CHASM FDR	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	CGL driver class	S.O. transcript	S.O. transcript strand	S.O. all transcripts	CGC driver class	CGC inheritance	CGC tumor types somatic	CGC tumor types germline	CHASM transcript	CHASM score	All transcripts CHASM results	ClinVar disease identifier	ClinVar XRef	COSMIC transcript	COSMIC protein change	COSMIC variant count	ESP6500 AF (European American)	ESP6500 AF (African American)	HGVS Genomic	HGVS Protein	HGVS Protein All	NCI pathway hits	NCI pathway IDs	NCI pathway names
1	VAR516_unknown	chr1	156701052	+	C	T	unknown	CRABP2	MS	G24E			0.4176					1		0.0	4.07800406169e-06		2.98044825942e-05										../MuPIT_Interactive?gm=chr1:156701052										0				122.853	.	het	8	20	0.4		ENST00000368221.1	-	*ENST00000368221.1:G24E(MS),ENST00000621784.4:G24E(MS),ENST00000368222.7:G24E(MS)					ENST00000368221.1	0.358	*ENST00000368221.1:G24E(0.358:0.4176),ENST00000368222.7:G24E(0.358:0.4176),ENST00000621784.4:G24E(0.358:0.4176)						0	0	NC_000001.10:g.156701052C>T	ENST00000368221.1:p.Gly24Glu	*ENST00000368221.1:p.Gly24Glu,ENST00000621784.4:p.Gly24Glu,ENST00000368222.7:p.Gly24Glu	0		
2	VAR517_unknown	chr19	18856059	+	C	T	unknown	UPF1	MS	A571V	EAIDSPVSFLALHNQIR	EAIDSPVSFLVLHNQIR	0.0394			COSM3100527	large_intestine(1)	1		0.0													../MuPIT_Interactive?gm=chr19:18856059										0				10269.5	.	het	592	2379	0.248844052123		ENST00000599848.5	+	ENST00000262803.9:A560V(MS),*ENST00000599848.5:A571V(MS)					ENST00000262803.9	0.63	*ENST00000599848.5:A571V(0.61:0.0530),ENST00000262803.9:A560V(0.63:0.0394)			ENST00000262803	p.A560V (large_intestine 1)	1	0	0	NC_000019.10:g.18856059C>T	ENST00000599848.5:p.Ala571Val	ENST00000262803.9:p.Ala560Val,*ENST00000599848.5:p.Ala571Val	0