Description

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

Input

name:type
description
pattern

meta{:bash}

:map

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

clusters{:bash}

:file

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

*clusters.txt

meta2{:bash}

:map

Groovy Map containing information about the fasta file e.g. [ id:‘test’ ]

fasta{:bash}

:file

The reference FASTA file (mandatory when using CRAM files)

*.{fasta,fa}

mei_ref{:bash}

: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{:bash}

meta{:bash}

:map

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

*_MEIs.txt{:bash}

:file

Tab-delimited text file containing MEI calls

*_MEIs.txt

dels_tab{:bash}

meta{:bash}

:map

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

*_PredictedDeletions.txt{:bash}

:file

Tab-delimited text file containing predicted deletions

*_PredictedDeletions.txt

vcf{:bash}

meta{:bash}

:map

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

*.vcf{:bash}

:file

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

*.vcf

versions{:bash}

versions.yml{:bash}

:file

File containing software versions

versions.yml

Tools

scramble
CC

Soft Clipped Read Alignment Mapper

github.com/GeneDx/scramble
maintainer
Github user nvnieuwk
get in touch
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