recipe scramble

Soft Clipped Read Alignment Mapper

Homepage

https://github.com/GeneDx/scramble

License

CC

Recipe

/scramble/meta.yaml

Links

doi: 10.1038/s41436-020-0749-x

SCRAMble identifies clusters of soft clipped reads in a BAM file, builds consensus sequences, aligns to representative L1Ta, AluYa5, and SVA-E sequences, and outputs MEI calls

package scramble

Versions

1.0.1-1,  1.0.1-0

Depends

• bioconductor-rsamtools >=2.4.0

• htslib >=1.12,<1.13.0a0

• libgcc-ng >=9.3.0

• r-base >=4.0.3

• r-optparse >=1.6.6

• r-rblast >=0.99.1

• r-stringr >=1.4.0

Required By

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install scramble

and update with:

conda update scramble

or use the docker container:

docker pull quay.io/biocontainers/scramble:<tag>

(see scramble/tags for valid values for <tag>)

Notes

SCRAMble runs as a two-step process. First cluster_identifier is used to generate soft-clipped read cluster consensus sequences. Second, SCRAMble.R analyzes the cluster file for likely MEIs. Custom wrapper script scramble.sh is provided to help setting location of SCRAMble.R script, and values for --install-dir and --mei-refs params.

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