Description

Annotate a VCF file with another VCF file

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information regarding vcf file provided
e.g. [ id:‘test’, single_end

]

vcf (file)

VCF file

*.{vcf, vcf.gz}

vcf_tbi (file)

Tabix file for compressed vcf provided

*.{tbi}

meta2 (map)

Groovy map containing sample information regarding database provided

database (file)

Database for use to annotate

*.{vcf/vcf.gz}

dbs_tbi (file)

Tabix file for compressed database provided

*.{tbi}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

versions (file)

File containing software versions

versions.yml

vcf (file)

Variant Calling File annotated

*.{vcf}
author
Github user LlaneroHiboreo
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

snpsift
MIT

SnpSift is a toolbox that allows you to filter and manipulate annotated files

pcingola.github.io/SnpEff/ss_introduction https://github.com/pcingola/SnpEff 10.3389/fgene.2012.00035