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
Full Changelog: v0.8.0...v0.9.0
Contributors
jlac and skchronicles