Synopsis

Clinical pipeline for detecting gene fusions in RNAseq data utilising JAFFA. The pipeline optionally calls a classifier for B-Cell Acute Lymphocytic Leukaemia (based on AllSorts). As well as variant calling pipeline using Picard,GATK and VEP.

Prerequisites

• AllSorts
• bbmap
• blat
• bowtie2
• bpipe
• fastqc
• GATK
• JAFFA
• java
• perl
• Picard
• python
• samtools v1.1
• trimmomatic
• RNA-Seqc
• VEP

Code Example

On meerkat:

module load java
module load bpipe

mkdir -p ./batches/{BATCH}/data
cp /path/to/data/files/*.fastq.gz ./batches/{BATCH}/data/  ## or symlink (ln -s)

./pipeline/scripts/create_batch.sh {BATCH} B_ALL designs/B_ALL/B_ALL.bed

cd ./batches/{BATCH}/analysis
bpipe run ../../../pipeline/pipeline.groovy ../samples.txt

Motivation

Installation

Clone repository. Install tools into tools directory, or follow README.md for setup on meerkat.

Authors

• Rebecca Louise Evans - Initial work - beccyl

License

This project is licensed under GNU General Public License - see the LICENSE.md file for details.

Acknowledgments

• ssadedin - provided the framework for bpipe and cpipe
• nadiadavidson - provided the underlying JAFFA "Just another fusion finding algorithm" on which this project is based.
• Quarkins - provided the algorithm for random forest classifier
• JovMaksimovic - generic bpipe pipeline for rna-seq
• aliciaoshlack - Team Leader