gulnazzaidi/varscan repository overview

⁠VarScan 2.3.9 Docker Image

A Docker image containing VarScan with samtools and bcftools. Includes Bash and a Java runtime.

⁠Tool Versions

• VarScan: 2.3.9
• samtools: 1.3.1
• bcftools: 1.3
• Java: OpenJDK 17 (JRE)
• Shell: bash

⁠Run the Container

⁠Interactive shell

docker run --rm -it varscan:2.3.9

⁠Check installed tool versions

docker run --rm  gulnazzaidi/varscan:2.3.9 tool-versions.sh

⁠Usage

To mount current working directory containing BAM/FASTA files:

docker run --rm -it \
  -v $(pwd):/data \
  varscan:2.3.9 bash

All tools are in /usr/local/bin/

varscan --help 

java -jar /usr/local/bin/VarScan.v2.3.9.jar --help

samtools --help

/usr/local/bin/samtools --help

bcftools --help

/usr/local/bin/bcftools --help