/picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
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README.md

Build Status

A set of Java command line tools for manipulating high-throughput sequencing (HTS) data and formats.

Picard is implemented using the HTSJDK Java libraryHTSJDK, supporting accessing of common file formats, such as SAM and VCF, used for high-throughput sequencing data.

It's also possible to build a version of Picard that supports reading from GA4GH API, e.g. Google Genomics: 1.Fetch gatk-tools-java library from https://github.com/iliat/gatk-tools-java 2.Build: ant gatk-tools-java-picard-jar 3.Copy the resulting jar to lib/gatk-tools-java/ under Picard folder, e.g. cp dist/gatk-tools-java-picard-1.0.jar ../picard/lib/gatk-tools-java/ 4.Build Picard: ant -lib lib/ant package-commands-ga4gh 5.You can now run java -jar dist/picard.jar ViewSam
INPUT=https://www.googleapis.com/genomics/v1beta2/readgroupsets/CK256frpGBD44IWHwLP22R4/
GA4GH_CLIENT_SECRETS=../client_secrets.json

Please see the Picard Documentation for more information.