/gatk-tools-java

Tools for using Picard and GATK with the Google Genomics API.
  1. Java 97.3%
  2. Shell 2.7%
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README.md

gatk-tools-java

Tools for using Picard and GATK with Genomics API.

  • Common classes for getting Reads from GA4GH Genomics API and exposing them as SAMRecord "Iterable" resource.

  • Implementation of a custom reader that can be plugged into Picard tools to handle reading of the input data specified via a url and coming from GA4GH API.

  • A set of shell scripts (src/main/scripts) that demonstrate how to run Picard tools with Ga4GH custom reader.

  • Requires htsjdk version 1.128 and greater and Picard latest version (past this commit https://github.com/iliat/picard/commit/ebe987313d799d58b0673351b95d3ca91fed82bf).

  • You can download Picard from: http://broadinstitute.github.io/picard/ and build it according to the instructions.

Build:
To build with ant: ant gatk-tools-java-jar.

Note that examples below assume you have built with ant, it produces dist/gatk-tools-java-1.0.jar The following examples assume you have picard folder side by side with gatk-tools-java.

The typical command line would look like:

java -jar \  
-Dsamjdk.custom_reader=https://www.googleapis.com/genomics,<location of gatk-tools-java jar> \  
-Dga4gh.client_secrets=<location of client_secrets.json>  \   
dist/picard.jar <ToolName> \  
INPUT=<input url>

E.g

java -jar \
-Dsamjdk.custom_reader=https://www.googleapis.com/genomics,com.google.cloud.genomics.gatk.htsjdk.GA4GHReaderFactory,\
`pwd`/dist/gatk-tools-java-1.0.jar \  
-Dga4gh.client_secrets=client_secrets.json \  
../picard/dist/picard.jar ViewSam \  
INPUT=https://www.googleapis.com/genomics/v1beta2/readgroupsets/CK256frpGBD44IWHwLP22R4/

The test read group set used here is the ex1_sorted.bam that can be found in testdata/ folder.
The data has been uploaded to the cloud project: https://console.developers.google.com/storage/browser/gatk-tools-java/.

The dataset id is: 15448427866823121459 and the read group set id is CK256frpGBD44IWHwLP22R4.

To build with Maven: mvn compile mvn bundle:bundle.
Note that Maven build produces gatk-tools-java-1.1-SNAPSHOT.jar.

  • For Picard tools that have not yet been instrumented to work with a custom reader, you can use Ga4GHPicardRunner. It is a wrapper around Picard tools that allows for INPUTS into Picard tools to be ga4gh:// urls by consuming the data via the API and using pipes to send it to Picard tool.