A pipeline for detecting allelic imbalance from DNA and RNA seq reads
A snakemake pipeline for running the variant calling portion of the pipeline. It generates a filtered VCF of heterozygous sites from DNA seq reads.
A snakemake pipeline for running WASP. It generates an un-biased, filtered BAM file from RNA seq reads.
A snakemake pipeline for generating and analyzing counts of heterozygous sites and detecting significant allelic imbalance from DNA and RNA BAM files.
Required input for each snakemake pipeline
Defines a function for detecting allelic imbalance given count data. This code was adapted from @Arkosen
An R script that sets up the necessary data for calling allele_imbalance.r and then calls it. This script is called, in turn, by Snakefile-counts.
A 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.
Once you've installed snakemake and adapted the provided config files to your liking, you can execute each section of the pipeline individually using the snakemake command or all at once on an SGE cluster using the provided run-all.bash script.
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:
Whether or not you use the --use-conda option, you must manually install a number of R packages. The full list of such packages is at the top of the find_imbalance.r script.