Mercurial > repos > galaxyp > cravatool
annotate test-data/noncoding.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 #Non-coding Variant 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 16:42:38.411675 |
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 variant level. |
2c7bcc1219fc
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
diff
changeset
|
8 #hg38 genomic. |
2c7bcc1219fc
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
diff
changeset
|
9 #Breast |
2c7bcc1219fc
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
diff
changeset
|
10 #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
|
11 |
2c7bcc1219fc
Updated cravatool to version 1.0 with updated formatting and new CRAVAT target URL.
galaxyp
parents:
diff
changeset
|
12 Input line ID Chromosome Position Strand Reference base(s) Alternate base(s) Sample ID HUGO symbol Sequence ontology Protein sequence change CHASM p-value CHASM FDR ClinVar COSMIC ID COSMIC variant count (tissue) Number of samples with variant dbSNP ESP6500 AF (average) gnomAD AF Total gnomAD AF African gnomAD AF American gnomAD AF Ashkenazi Jewish gnomAD AF East Asian gnomAD AF Finnish gnomAD AF Non-Finnish European gnomAD AF Other gnomAD AF South Asian GWAS NHLBI Key (GRASP) GWAS PMID (GRASP) GWAS Phenotype (GRASP) Protein 3D variant In TCGA Mutation Cluster ncRNA Class ncRNA Name Pseudogene Pseudogene Transcript Repeat Class Repeat Family Repeat Name TARGET 1000 Genomes AF UTR/Intron UTR/Intron Gene UTR/Intron All Transcript Phred VCF filters Zygosity Alternate reads Total reads Variant allele frequency CGL driver class |