Description

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

inputs (file(s))

One or more input BAM/CRAM file(s)

*.{bam,cram}

assembly (file)

OPTIONAL - An assembly BAM file created by the assembly step of Gridss

*.bam

fasta (file)

The reference fasta

*.{fa,fna,fasta}

fasta_fai (file)

The index of the reference fasta

*.fai

bwa_index (directory)

OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step

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)

The called VCF file created by Gridss’ call step

*.vcf.gz

assembly (file)

The assembly BAM file created by Gridss’ assembly step

*.assembly.bam
author
Github user nvnieuwk
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Tools

gridss
GPL v3

GRIDSS: the Genomic Rearrangement IDentification Software Suite

github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation https://github.com/PapenfussLab/gridss 10.1186/s13059-021-02423-x