FixItFelix: improving genomic analysis by fixing reference errors

The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an e...

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Detalles Bibliográficos
Autores principales: Behera, Sairam, LeFaive, Jonathon, Orchard, Peter, Mahmoud, Medhat, Paulin, Luis F., Farek, Jesse, Soto, Daniela C., Parker, Stephen C. J., Smith, Albert V., Dennis, Megan Y., Zook, Justin M., Sedlazeck, Fritz J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2023
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9942314/
https://www.ncbi.nlm.nih.gov/pubmed/36810122
http://dx.doi.org/10.1186/s13059-023-02863-7
Descripción
Sumario:The current version of the human reference genome, GRCh38, contains a number of errors including 1.2 Mbp of falsely duplicated and 8.04 Mbp of collapsed regions. These errors impact the variant calling of 33 protein-coding genes, including 12 with medical relevance. Here, we present FixItFelix, an efficient remapping approach, together with a modified version of the GRCh38 reference genome that improves the subsequent analysis across these genes within minutes for an existing alignment file while maintaining the same coordinates. We showcase these improvements over multi-ethnic control samples, demonstrating improvements for population variant calling as well as eQTL studies. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-023-02863-7.

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