Filter variants based on Ensembl Variant Effect Predictor (VEP) annotations.
Input
name:type
description
pattern
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
input
:file
VCF/TAB file annotated with vep
*.{vcf,tab,tsv,txt}
feature_file
:file
File containing features on separate lines. To be used with —filter option.
Output
name:type
description
pattern
output
meta
:map
Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]
*.${extension}
:file
VCF/TAB file
*.{vcf,tab,txt,tsv}
versions_ensemblvep
${task.process}
:string
The process the versions were collected from
ensemblvep
:string
The tool name
vep --help | sed -n '/ensembl-vep/s/.*: //p'
:eval
The command used to generate the version of the tool
versions_perlmathcdf
${task.process}
:string
The process the versions were collected from
perl-math-cdf
:string
The tool name
perl -MMath::CDF -e 'print \\$Math::CDF::VERSION'
:eval
The expression to obtain the version of the tool
Topics
name:type
description
pattern
versions
${task.process}
:string
The process the versions were collected from
ensemblvep
:string
The tool name
vep --help | sed -n '/ensembl-vep/s/.*: //p'
:eval
The command used to generate the version of the tool
${task.process}
:string
The process the versions were collected from
perl-math-cdf
:string
The tool name
perl -MMath::CDF -e 'print \\$Math::CDF::VERSION'
:eval
The expression to obtain the version of the tool
Tools
ensemblvep
Apache-2.0
VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs
or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
