pegi3s/picard 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 Picard⁠, a set of command line tools for manipulating high-throughput sequencing data and formats such as SAM/BAM/CRAM and VCF.

This toolset can be used to perform the following operations:

• Base Calling: tools that process sequencing machine data and detect sequencing level attributes.
• Diagnostics and Quality Control: tools that collect sequencing quality related and comparative metrics.
• Genotyping Arrays Manipulation: tools that manipulate data generated by genotyping arrays.
• Intervals Manipulation: tools that process genomic intervals in various formats.
• Read Data Manipulation: tools that manipulate read data in SAM, BAM or CRAM format.
• Reference: tools that analyze and manipulate FASTA format references.
• Variant Evaluation and Refinement: tools that evaluate and refine variant calls.
• Variant Filtering: tools that filter variants by annotating the FILTER column.
• Variant Manipulation: tools that manipulate variant call format (VCF) data.
• Other: Miscellaneous tools.

To see Picard options, just run docker run --rm pegi3s/picard -h.

⁠Using the Picard image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/picard <picard-application-name> <options>

In this command, you should replace:

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

For instance, to clean a SAM file, you should run: docker run --rm -v /your/data/dir:/data pegi3s/picard CleanSam -I /data/aln-pe.sam -O /data/aln-pe_cleaned.sam