michaelfranklin/vardict repository overview

⁠Quickstart

Run: docker run -it --entrypoint /bin/bash michaelfranklin/vardict:1.6.0

And then within the container: VarDict

⁠Highlights:

• vardict/bin is exported in path
• Just call VarDict to access the Java port of VarDict⁠
• BCFTools is included in the container from v1.6.0 in order to easily compress the VCF output.

You can also call other files packaged in the release tarball:

• testsomatic.R
• teststrandbias.R
• var2vcf_paired.pl var2vcf_valid.pl

⁠Introduction

VarDictJava is a variant discovery program for both single and paired sample variant calling from BAM files. This Docker specifically containerises the Java port of the original VarDict variant caller. Per the requirements, this container also installs, R language and Perl.

• VarDictJava Repository: https://github.com/AstraZeneca-NGS/VarDictJava⁠

Note, the VarDictJava program is licensed under the MIT license (at time of publishing), more information can be found on AstraZeneca-NGS/VarDictJava README⁠, the Dockerfile is also licensed under the MIT License.

For transparency, VarDict is downloaded, and unarchived to the/opt/vardict/ directory, and the bin directory (/opt/vardict/bin) has been added to $PATH. This means you can call VarDict, or any of the other files that are contained within the release tarball (testsomatic.R teststrandbias.R var2vcf_paired.pl var2vcf_valid.pl). VarDict is additionally added as the entrypoint to the Docker.

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Other versions of this tool can be created by changing the VARDICT_VERSION environment variable within the Dockerfile.

This Dockerfile uses ubuntu:16.04⁠ as a base as it's a common, small-ish repository that is likely already archived by your computer.