Genetic variant annotation and functional effect prediction toolbox
Input
name:type
description
pattern
meta{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
vcf{:bash}
:file
vcf to annotate
db{:bash}
:string
which db to annotate with
meta2{:bash}
:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end:false ]
cache{:bash}
:file
path to snpEff cache (optional)
Output
name:type
description
pattern
vcf{:bash}
meta{:bash}
:file
annotated vcf
*.ann.vcf
*.ann.vcf{:bash}
:file
annotated vcf
*.ann.vcf
report{:bash}
meta{:bash}
:file
annotated vcf
*.ann.vcf
*.csv{:bash}
:file
snpEff report csv file
*.csv
summary_html{:bash}
meta{:bash}
:file
annotated vcf
*.ann.vcf
*.html{:bash}
:file
snpEff summary statistics in html file
*.html
genes_txt{:bash}
meta{:bash}
:file
annotated vcf
*.ann.vcf
*.genes.txt{:bash}
:file
txt (tab separated) file having counts of the number of variants affecting each transcript and gene
*.genes.txt
versions{:bash}
versions.yml{:bash}
:file
File containing software versions
versions.yml
Tools
snpeff
MIT
SnpEff is a variant annotation and effect prediction tool.
It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes).
