cravatool: test-data/gene.tsv annotate

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

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

rev	line source
1 2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	1 #Gene Level Annotation Report
3 a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty galaxyp parents: 1 diff changeset	2 #2018-09-07 16:42:38.415811
1 2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	3 #CRAVAT version: hybrid
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	4 #Analysis done at http://www.cravat.us.
3 a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty galaxyp parents: 1 diff changeset	5 #Job Id: rsajulga_20180907_124216
a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty galaxyp parents: 1 diff changeset	6 #Input file: Freebayes_one_variant.vcf
1 2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	7 #This report shows analysis results at gene level.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	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.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	9 #hg38 genomic.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	10 #Breast
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	11 #For more information on CRAVAT, visit http://www.cravat.us.
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	12
2c7bcc1219fc Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL. galaxyp parents: diff changeset	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
3 a018c44dc18b planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/cravatp_score_and_annotate commit d80e60ce74aabe64e131d560085af099d52b81cf-dirty galaxyp parents: 1 diff changeset	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