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}

tbi:list

List of VCF file indexes

*.{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

meta:file

Compressed VCF file

*.vcf.gz

*.vcf.gz:file

Compressed VCF file

*.vcf.gz

tbi

meta:file

Index of VCF file

*.vcf.gz.tbi

*.tbi:file

Index of VCF file

*.vcf.gz.tbi

versions

versions.yml:file

File containing software versions

versions.yml

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
included in
pathogensurveillance raredisease rnadnavar rnavar variantcatalogue
maintainers
Github user kevinmenden
Github user ramprasadn
get in touch
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