Implementation of Indel and Multiallelic Variant Normalization in Sarek Pipeline

[Patricie34]

Description of feature

Dear Sarek Development Team,

I am writing on behalf of our research group, which uses the Sarek pipeline for WGS data analysis. We are currently exploring ways to optimize our workflow and have identified the need to include a normalization step for indels and multiallelic variants directly within the pipeline.

In our research, we compare data generated from different pipelines and have encountered discrepancies in how indels are represented. This complicates downstream analysis, as the unnormalized indels often lack proper annotations. To address this, we use bcftools for normalization, but after this process, the annotations are lost, requiring a reannotation step.

To streamline our workflow, we believe it would be highly beneficial to include the normalization step immediately after variant calling and before annotation with VEP. This would ensure consistent variant representation without needing reannotation after normalization.

We have had great experiences running Sarek on our cluster, and it has become an integral part of our work. We have no intention of switching pipelines, and we plan to continue using Sarek in our upcoming projects. For these reasons, we believe adding this normalization step would further improve the efficiency of our research process.

We would like to inquire whether this feature could be integrated into Sarek, or if you might have suggestions on how to implement it. We would be happy to collaborate or provide feedback as necessary.

Thank you for your attention, and we look forward to your response.

Best regards,

Patricie