Mercurial > repos > galaxyp > cravatool
comparison test-data/gene.tsv @ 1:2c7bcc1219fc draft
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
| author | galaxyp |
|---|---|
| date | Thu, 16 Aug 2018 12:27:35 -0400 |
| parents | |
| children | a018c44dc18b |
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| 0:83181dabeb90 | 1:2c7bcc1219fc |
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| 1 #Gene Level Annotation Report | |
| 2 #2018-08-13 15:36:32.359533 | |
| 3 #CRAVAT version: hybrid | |
| 4 #Analysis done at http://www.cravat.us. | |
| 5 #Job Id: rsajulga_20180813_113614 | |
| 6 #Input file: Freebayes_two_variants.vcf | |
| 7 #This report shows analysis results at gene level. | |
| 8 #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. | |
| 9 #hg38 genomic. | |
| 10 #Breast | |
| 11 #For more information on CRAVAT, visit http://www.cravat.us. | |
| 12 | |
| 13 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 | |
| 14 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 | |
| 15 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 |