Description

Apply tranche filtering

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcf (file)

a VCF file containing variants, must have info key

*.vcf.gz

tbi (file)

tbi file matching with -vcf

*.vcf.gz.tbi

resources (list)

resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary

*.vcf.gz

resources_index (list)

Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary

*.vcf.gz

fasta (file)

The reference fasta file

*.fasta

fai (file)

Index of reference fasta file

fasta.fai

dict (file)

GATK sequence dictionary

.dict

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)

VCF file

*.vcf.gz

tbi (file)

VCF index file

*.vcf.gz.tbi
included in
sarek
maintainer
Github user FriederikeHanssen
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/articles/360051308071-FilterVariantTranches 10.1158/1538-7445.AM2017-3590