pegi3s/gatk-4 repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of GATK 4⁠, the industry standard for identifying SNPs and indels in germline DNA and RNAseq data. Its scope is now expanding to include somatic short variant calling, and to tackle copy number (CNV) and structural variation (SV). In addition to the variant callers themselves, the GATK also includes many utilities to perform related tasks such as processing and quality control of high-throughput sequencing data, and bundles the popular Picard toolkit.

To see GATK 4 available tools, just run docker run --rm pegi3s/gatk-4:4.7.0.0 gatk --list. Please note that GATK 4 does not include some tools that are included in GATK 3⁠.

To obtain the help of a particular tool, you just need to run: docker run --rm pegi3s/gatk-4:4.7.0.0 gatk <tools> --help (e.g. docker run --rm pegi3s/gatk-4:4.7.0.0 gatk SortVcf --help)

⁠Using the GATK 4 image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/gatk-4:4.7.0.0 gatk <tools> <options>

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <tools> to the name of the GATK 4 tool you want to use.
• <options> with the specific options of the GATK 4 tool. These options will include the input/output files, which should be referenced under /data/.

For instance, to sort a VCF file using GATK 4, you should run: docker run --rm -v /your/data/dir:/data pegi3s/gatk-4:4.7.0.0 gatk SortVcf -I /data/test.recode.vcf -O /data/test_sorted.recode.vcf

⁠Test data

To test the previous command, the VCF file used is available here⁠.

⁠Using the GATK 4 image in Windows

Please note that data must be under the same drive than the Docker Toolbox installation (usually C:) and in a folder with write permissions (e.g. C:/Users/User_name/).

As in the Linux case, to run an application, you should adapt and run the following command: docker run --rm -v "/c/Users/User_name/dir/":/data pegi3s/gatk-4:4.7.0.0 gatk <tools> <options>