Description

Clusters structural variants based on coordinates, event type, and supporting algorithms

Input

Name (Type)
Description
Pattern

meta (map)

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

]

vcfs (file)

One or more VCF files created with a structural variant caller

*.vcf.gz

indices (file)

Index files for the VCFs

*.vcf.gz.tbi

ploidy_table (file)

The sample ploidy table

*.tsv

fasta (file)

Reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

fasta_fai (file)

Index of the reference FASTA file needed when the input is a CRAM file

*.fai

dict (file)

Sequence dictionary of the reference FASTA file needed when the input is a CRAM file

*.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

clustered_vcf (file)

The VCF containing the clustered VCFs

*.vcf.gz

clustered_vcf_index (file)

The index of the VCF containing the clustered VCFs

*.vcf.gz.tbi
author
Github user nvnieuwk
get in touch
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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 github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590