Abstract

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.

Details

Title
FixItFelix: improving genomic analysis by fixing reference errors
Author
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
Pages
1-21
Section
Method
Publication year
2023
Publication date
2023
Publisher
BioMed Central
ISSN
14747596
e-ISSN
1474760X
Source type
Scholarly Journal
Language of publication
English
ProQuest document ID
2788484197
Copyright
© 2023. This work is licensed under http://creativecommons.org/licenses/by/4.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.