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:false ]

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

meis_tab

meta:map

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

*_MEIs.txt:file

Tab-delimited text file containing MEI calls

*_MEIs.txt

dels_tab

meta:map

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

*_PredictedDeletions.txt:file

Tab-delimited text file containing predicted deletions

*_PredictedDeletions.txt

vcf

meta:map

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

*.vcf:file

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

*.vcf

versions

versions.yml:file

File containing software versions

versions.yml

Tools

scramble
CC

Soft Clipped Read Alignment Mapper

github.com/GeneDx/scramble
Github user nvnieuwk
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