frogsicle / 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.

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

Picard is implemented using the HTSJDK Java library HTSJDK to support accessing file formats that are commonly used for high-throughput sequencing data such as SAM and VCF.

As of version 2.0.1 (Nov. 2015) Picard requires Java 1.8 (jdk8u66). The last version to support Java 1.7 was release 1.141.

To clone and build: Clone the repo:

git clone [email protected]:broadinstitute/picard.git
cd picard/

Clone htsjdk into a subdirectory:

ant clone-htsjdk

Build:

ant

Enjoy!

java -jar dist/picard.jar

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It's also possible to build a version of Picard that supports reading from GA4GH API, e.g. Google Genomics:

• Fetch gatk-tools-java

git clone https://github.com/googlegenomics/gatk-tools-java

• Build gatk-tools-java:

gatk-tools-java$ mvn compile package

• Copy the resulting jar into Picard lib/ folder:

gatk-tools-java$ mkdir ../picard/lib/gatk-tools-java
gatk-tools-java$ cp target/gatk-tools-java*minimized.jar ../picard/lib/gatk-tools-java/

• Build Picard version with GA4GH support:

picard$ ant -lib lib/ant package-commands-ga4gh

• If you have not yet worked with Google Genomics API and need to set up authentication, please follow the instructions here to set up credentials and obtain client_secrets.json file.

• 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

• To run using GRPC as opposed to REST Genomics API implementation (which is much faster) use the following command that utilizes ALPN jars that come with gatk-tools-java and enables GRPC support:

java \
-Xbootclasspath/p:../gatk-tools-java/lib/alpn-boot-8.1.3.v20150130.jar \
-Dga4gh.using_grpc=true \
-jar dist/picard.jar ViewSam \
INPUT=https://www.googleapis.com/genomics/v1beta2/readgroupsets/CK256frpGBD44IWHwLP22R4/ \
GA4GH_CLIENT_SECRETS=../client_secrets.json

For Java 7 (as opposed to 8) use alpn-boot-7.1.3.v20150130.jar.

Picard is migrating to semantic versioning (http://semver.org/). We will eventually adhere to it strictly and bump our major version whenever there are breaking changes to our API, but until we more clearly define what constitutes our official API, clients should assume that every release potentially contains at least minor changes to public methods.

Please see the Picard Documentation for more information.