Name
GA4GH Technical Team: Current Accomplishments and Future Plans
Description

As part of our strategic plan, the GA4GH aims to hire a core technical team of software developers, led by a Chief Standards Officer. Based at multiple host institutions (Ontario Institute for Cancer Research, Broad Institute, Wellcome Sanger Institute, and EMBL-EBI), this team will be dedicated to the widespread uptake of GA4GH specifications. The team will develop a variety of open source tools, including reference implementations of GA4GH APIs, client libraries for accessing data from compliant web services, and applications for reading and writing standardized file formats (e.g. CRAM, Crypt4GH) or structured messages (e.g. Phenopackets, Variant Representation). Wherever possible, this software will be integrated into widely-used bioinformatics toolkits, such as the Genome Analysis Toolkit (GATK), samtools, htsjdk, and htslib, allowing researchers to seamlessly have their existing workflows work with GA4GH-based APIs and datasets. As GA4GH web services can be viewed as a large-scale, federated network in which multiple institutions agree to share data under common protocols, the team of core developers will create registries and testbeds to monitor the network and assess compliance of nodes to specifications. Over the past year, an early version of this team has developed a number of resources for several key deliverables. The GA4GH Planet API is a publicly-available service registry, serving metadata about running GA4GH-compliant deployments from around the world and across institutional boundaries. The team has also developed htsget client support in both GATK and htsjdk, allowing researchers to run GATK analysis walkers using alignment or variant files behind htsget services. A lightweight htsget reference server allows new features to be proposed and prototyped quickly, and also serves as the test source for the GATK and htsjdk clients to run against.

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