Picard
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Introduction
Picard is a set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. These file formats are defined in the Hts-specs repository. See especially the SAM specification and the VCF specification.
Installed version
Using Picard on the HPC cluster
Documentation
You can find the full documentation