Description

Filter variants

Input

Name (Type)
Description
Pattern

meta (map)

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

vcf (list)

List of VCF(.gz) files

*.{vcf,vcf.gz}

vcf_tbi (list)

List of VCF file indexes

*.{idx,tbi}

meta2 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fasta (file)

Fasta file of reference genome

*.fasta

meta3 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

fai (file)

Index of fasta file

*.fasta.fai

meta4 (map)

Groovy Map containing reference information
e.g. [ id:‘genome’ ]

dict (file)

Sequence dictionary of fastea file

*.dict

Output

Name (Type)
Description
Pattern

vcf (file)

Compressed VCF file

*.vcf.gz

tbi (file)

Index of VCF file

*.vcf.gz.tbi

versions (file)

File containing software versions

versions.yml
included in
pathogensurveillance raredisease rnadnavar rnavar variantcatalogue
maintainers
Github user kevinmenden
Github user ramprasadn
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

gatk4
Apache-2.0

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.

gatk.broadinstitute.org/hc/en-us gatk.broadinstitute.org/hc/en-us/categories/360002369672s 10.1158/1538-7445.AM2017-3590