Genetic variant annotation and functional effect prediction toolbox
Input
name:type
description
pattern
meta:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
vcf:file
vcf to annotate
db:string
which db to annotate with
meta2:map
Groovy Map containing sample information
e.g. [ id:‘test’, single_end
]
cache:file
path to snpEff cache (optional)
Output
name:type
description
pattern
vcf
meta:file
annotated vcf
*.ann.vcf
*.ann.vcf:file
annotated vcf
*.ann.vcf
report
meta:file
snpEff report csv file
*.csv
*.csv:file
snpEff report csv file
*.csv
summary_html
meta:file
snpEff summary statistics in html file
*.html
*.html:file
snpEff summary statistics in html file
*.html
genes_txt
meta:file
txt (tab separated) file having counts of the number of variants affecting each transcript and gene
*.genes.txt
*.genes.txt:file
txt (tab separated) file having counts of the number of variants affecting each transcript and gene
*.genes.txt
versions
versions.yml: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).
