Snakemake workflow: generating a synthetic tumor/normal dataset from the haploid cell lines CHM1 and CHM13

This workflow generates a synthetic tumor/normal dataset based on the syndip benchmark.

Authors

• Johannes Köster (@johanneskoester)

Usage

In any case, if you use this workflow in a paper, don't forget to give credits to the authors (and the authors of the syndip benchmark) by citing the URL of this (original) repository.

Perform a dry-run via

snakemake --use-conda -n

Execute the workflow locally via

snakemake --use-conda --cores $N

using $N cores or run it in a cluster environment via

snakemake --use-conda --cluster qsub --jobs 100

or

snakemake --use-conda --drmaa --jobs 100

See the Snakemake documentation for further details.