Mercurial > repos > galaxyp > cravatool

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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