duxhund

DUX4 fusions finder

Overview

Duxhund is a dedicated tool to call DUX4 fusions. It calls DUX4 fusions by the following three steps:

• Align the input reads by BWA
• Cut off softclips from the alignments and realign them with BWA, using a reference sequence that masks the pseudo-gene regions of DUX4
• Extract appropriate triplets of alignments from the realigned result and call them with fusionfusion

Prerequisites

For running from the command line

• BWA
• samtools
• fusionfusion
• Java JDK (>= 8)
• Leiningen (to build Clojure code)

For running in a Docker container

• Docker

Usage

Duxhund provides the following scripts:

• duxhund.sh: to run from the command line
• duxhund_batch.sh to run as an AWS Batch job

Running duxhund.sh script

The duxhund.sh script supports two ways to run:

• To run in a Docker container
• To run directly from the command line

Running in Docker container

To run duxhund.sh in a Docker container, you'll need to build the Docker image first. To build the Docker image, run:

./script/build.sh

Or, if you would like to name the resulting image, run:

IMAGE_NAME=<image name> ./script/build.sh

By default, the image name will be chrovis/duxhund:latest.

Once you build the image, you can run duxhund.sh as:

docker run <image name> duxhund.sh <arg> ...

Running directly from command line

To run duxhund.sh directly from the command line, you'll need to build the Clojure code first. To build it, run:

lein uberjar

After the Clojure code is successfully built, the duxhund.jar file will be generated in the target directory.

To run duxhund.sh, run:

DUXHUND_JAR=<duxhund.jar path> duxhund.sh <arg> ...

If you have the dependant tools (i.e. BWA, samtools and fusionfusion) installed not on your PATH, you'll need to specify their installation paths in addition:

BWA=<bwa path> SAMTOOLS=<samtools path> \
FUSIONFUSION=<fusionfusion path> DUXHUND_JAR=<duxhund.jar path> duxhund.sh <arg> ...

Options for duxhund.sh

The duxhund.sh script takes the following options as the command line arguments, which are all mandatory:

• --reference: The path to the reference FASTA file
• --masked-reference: The path to the masked reference FASTA file (see below for details)
• --target: The path to the target BED file
• --r1, --r2: The paths to the input FASTQ files
• --output: The path to the output directory

How to make a masked reference

A masked reference is a reference that is masked for the regions of DUX4 pseudo-genes. To make a masked reference, run the following commands:

$ bedtools maskfasta \
  -fi <input FASTA file> \
  -bed <DUX4 pseudo-gene BED file> \
  -fo <output FASTA file>
$ bwa index <output FASTA file>

Duxhund bundles the DUX4 pseudo-gene BED file in the resources/ directory.

License

Copyright © 2021 Xcoo, Inc.

This program is distributed under the GNU General Public License v3. See LICENSE for details.