pegi3s/gatk-3 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 3⁠, 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 3 options and available tools, just run docker run --rm pegi3s/gatk-3:3.8-0 java -jar /opt/GenomeAnalysisTK.jar -h.

⁠Using the GATK 3 image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/gatk-3:3.8-0 java -jar /opt/GenomeAnalysisTK.jar <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 3 tool you want to use.
• <options> with the specific options of the GATK 3 tool. These options will include the input/output files, which should be referenced under /data/.

For instance, to generate a target list of InDel positions using GATK 3, you should run: docker run --rm -v /your/data/dir:/data pegi3s/gatk-3:3.8-0 java -jar /opt/GenomeAnalysisTK.jar -T RealignerTargetCreator -R /data/chr19_KI270866v1_alt.fasta -I /data/aln-pe_out_sorted.bam -o /data/aln-pe_out_sorted.list

⁠Test data

To test the previous command, all the required files are available here⁠.