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

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

#Gene Level Annotation Report
#2018-08-13 15:36:32.359533
#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 gene level.
#The composite p-value (Stouffer's combined p-value) and composite FDR of a gene show how probable it is to get the same p-value distribution for the gene as that obtained from the input variants by chance.
#hg38 genomic.
#Breast
#For more information on CRAVAT, visit http://www.cravat.us.

HUGO symbol	Number of variants	Sequence ontology	CGC driver class	CGC inheritance	CGC tumor types somatic	CGC tumor types germline	ClinVar disease identifier	ClinVar XRef	Occurrences in COSMIC	COSMIC gene count (tissue)	Number of samples with gene mutated	CHASM gene score	CHASM gene p-value	CHASM gene FDR	VEST gene score (non-silent)	VEST gene p-value	VEST gene FDR	Protein 3D gene	Has a mutation in a TCGA Mutation Cluster	NCI pathway hits	NCI pathway IDs	NCI pathway names	TARGET	CGL driver class
CRABP2	1	MS							37	upper_aerodigestive_tract(3);large_intestine(9);stomach(4);soft_tissue(3);endometrium(4);lung(3);liver(2);skin(4);NS(1);prostate(1);bone(1);kidney(1);breast(1)	1	0.358	0.4176	1				../MuPIT_Interactive?gm=chr1:156701052		0				
UPF1	1	MS							267	large_intestine(57);endometrium(18);lung(13);skin(45);meninges(1);kidney(9);thyroid(3);cervix(4);central_nervous_system(7);oesophagus(5);NS(4);upper_aerodigestive_tract(10);biliary_tract(2);stomach(15);soft_tissue(6);urinary_tract(12);breast(11);prostate(7);pancreas(7);haematopoietic_and_lymphoid_tissue(10);ovary(4);bone(2);liver(15)	1	0.63	0.0394	0.1				../MuPIT_Interactive?gm=chr19:18856059		0