A Snakemake pipeline for detecting allelic imbalance from DNA and RNA seq reads
A Snakemake pipeline defining rules for every step of the analysis. It uses DNA and RNA FASTQ files to generate a summary of allelic imbalance for each gene.
Defines options and input for the Snakemake pipeline.
An example bash script for executing the entire pipeline on an SGE cluster using snakemake.
The pipeline is written as Snakefiles and so can be executed via Snakemake. See the run-all.bash script for an example. Make sure to provide required input and options in the config file before executing. For more information about what is required in the config file, see the READMEs for each portion of the pipeline.
The entire pipeline is made up of three different sections. We provide a single Snakefile to execute all of them at once, but you can also execute each of these sections on their own. For each section that you'd like to run separately, you must fill out a new config file. You can find more information about these individual portions of the pipeline and how to execute them in the Snakefiles directory.
By default, the pipeline will automatically delete some files it deems unnecessary (ex: unsorted copies of a BAM). You can opt to keep these files instead by providing the --notemp flag to Snakemake when executing the pipeline.
If you have Anaconda installed (highly recommended), use the --use-conda flag when calling snakemake to let it automatically handle all dependencies of the pipeline. Otherwise, you must manually install the following dependencies:
Note that our pipeline uses WASP (v3.x), which is not available from Anaconda. If the pipeline is unable to locate WASP, it will automatically install it. The --use-conda option will automatically handle WASP's dependencies, but you can see the WASP README if you'd like to install these dependencies manually.