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Release 13
The aim for BALSAMIC 13 is to start the validation work at the end of May.
The features planned for implementation are prioritised in here, with the highest priority features being developed first. Our intention is for the planned features to be part of the coming release. However, we can not guarantee that all features will make it into the final release.
Tumor mutation burden
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CADD scores
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Somatic Impact scores
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Copy number - Loss of heterozygosity
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GENS support
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Restructuring core alignment workflow
- Pre-processing and alignment of reads is done in parallel per sequencing lane to speed up analysis (primarily affecting WGS cases) and add lane information for improved variant-calling.
- Alignment workflow unified across TGA, WES and WGS to only use Sentieon tools.
Improved handling of validation cases
Validation cases should be readily accessible during the testing on stage environment to avoid the need for repeated decompression and storage of FASTQs.
Deployment tools
Ensure a smoother validation and deployment by:
- Only deploying to production what has been thoroughly tested and validated in the staging environment
- Submit reference and container download jobs to Slurm, a job scheduling system, to streamline the deployment process and improve efficiency
- Address all known bugs and update any outdated software versions to ensure optimal performance and reduce the risk of errors during deployment
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