Description

The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by cluster_identifier

Input

Name (Type)
Description
Pattern

meta (map)

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

]

clusters (file)

Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier

*clusters.txt

fasta (file)

Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions.

*.{fasta,fa}

mei_ref (file)

Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn’t correct

*.{fasta,fa}

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

meis_tab (file)

Tab-delimited text file containing MEI calls

*_MEIs.txt

dels_tab (file)

Tab-delimited text file containing predicted deletions

*_PredictedDeletions.txt

vcf (file)

A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments)

*.vcf

Tools

scramble
CC

Soft Clipped Read Alignment Mapper