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:false ]

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

clustered_vcf

meta:map

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

*.vcf.gz:file

The VCF containing the clustered VCFs

*.vcf.gz

clustered_vcf_index

meta:map

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

*.vcf.gz.tbi:file

The index of the VCF containing the clustered VCFs

*.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 github.com/broadinstitute/gatk 10.1158/1538-7445.AM2017-3590
Github user nvnieuwk
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