picard

Picard is a set of tools for the manipulation of high-throughput sequencing data and formats such as SAM, BAM, CRAM, and VCF.

Contains tools for the following areas of analysis:

Area of Analysis	Description
Base calling	Tools that process sequencing machine data e.g. Illumina base calls and detect sequencing level attributes, e.g. adapters
Diagnostics and QC	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
Other	Miscellaneous tools e.g. those that aid in data streaming
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, e.g. with annotations not offered by the engine
Variant filtering	Tools that filter variants by annotating the FILTER column
Variant manipulation	Tools that manipulate variant call format data

Users are urged to refer to the documentation for additional information and examples.

Parallel Capabilities: Single core only.