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comparison test-data/gene.tsv @ 3:a018c44dc18b draft default tip

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty
author galaxyp
date Fri, 07 Sep 2018 16:53:05 -0400
parents 2c7bcc1219fc
children
comparison
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2:f3027b8f28bd 3:a018c44dc18b
1 #Gene Level Annotation Report 1 #Gene Level Annotation Report
2 #2018-08-13 15:36:32.359533 2 #2018-09-07 16:42:38.415811
3 #CRAVAT version: hybrid 3 #CRAVAT version: hybrid
4 #Analysis done at http://www.cravat.us. 4 #Analysis done at http://www.cravat.us.
5 #Job Id: rsajulga_20180813_113614 5 #Job Id: rsajulga_20180907_124216
6 #Input file: Freebayes_two_variants.vcf 6 #Input file: Freebayes_one_variant.vcf
7 #This report shows analysis results at gene level. 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. 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. 9 #hg38 genomic.
10 #Breast 10 #Breast
11 #For more information on CRAVAT, visit http://www.cravat.us. 11 #For more information on CRAVAT, visit http://www.cravat.us.
12 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 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 14 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 1 ../MuPIT_Interactive?gm=chr19:18856059 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