v0.9.0

genome-seek (v0.9.0)

A new minor release of the genome-seek pipeline!

What's changed

This release contains a new optional sub-workflow to call short germline variants (SNPs + Indels) using GATK4's set of recommended best practices. To enable the GATK germline pipeline, please provide the following option: --gatk-germline.

By default, i.e. if this option is not provided, the pipeline will call short germline variants using deepvariant. If this option is provided, it will call germline variants with GATK4's HaplotypeCaller and deepvariant.

Benchmarking

The GATK4 germline pipeline was benchmarked with GAIB sample HG002. For more information and the results, please see issue #21.

Contributors

@jlac, @skchronicles

Full Changelog: v0.8.0...v0.9.0

v0.6.0

genome-seek (v0.6.0)

First public release of the genome-seek pipeline!

genome-seek is a comprehensive clinical WGS pipeline that is focused on speed. Each tool in the pipeline was benchmarked and selected due to its low run times without sacrificing accuracy or precision. genome-seek run can be used to call germline and somatic variants, infer SVs & CNVs, call hla-types, annotate variants, and much more!

The pipeline also runs a comprehensive set of quality-control tools so you can assess the quality of your data.

What's Changed

• Changes to calling and merging somatic variants by @jlac and @skchronicles in #15

Contributors

@jlac, @KeyTals, @skchronicles

Full Changelog: https://github.com/OpenOmics/genome-seek/commits/v0.6.0