Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

vcfs{:bash}

:file

One or more VCF files created with a structural variant caller

*.vcf.gz

indices{:bash}

:file

Index files for the VCFs

*.vcf.gz.tbi

ploidy_table{:bash}

:file

The sample ploidy table

*.tsv

fasta{:bash}

:file

Reference FASTA file needed when the input is a CRAM file

*.{fasta,fa}

fasta_fai{:bash}

:file

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

*.fai

dict{:bash}

:file

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

*.dict

Output

name:type
description
pattern

clustered_vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

The VCF containing the clustered VCFs

*.vcf.gz

clustered_vcf_index{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

The index of the VCF containing the clustered VCFs

*.vcf.gz.tbi

versions{:bash}

versions.yml{:bash}

: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 github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
maintainer
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub