picsaver / picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

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.

To clone and build: Clone the repo:

git clone [e-mail]:broadinstitute/picard.git
cd picard/

Clone htsjdk into a subdirectory:

ant clone-htsjdk

Build:

ant

Enjoy!

java -jar dist/picard.jar

---

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.

Please see the Picard Documentation for more information.