FixItFelix: improving genomic analysis by fixing reference errors.

TitleFixItFelix: improving genomic analysis by fixing reference errors.
Publication TypeJournal Article
Year of Publication2023
AuthorsBehera, S, LeFaive, J, Orchard, P, Mahmoud, M, Paulin, LF, Farek, J, Soto, DC, Parker, SCJ, Smith, AV, Dennis, MY, Zook, JM, Sedlazeck, FJ
JournalGenome Biol
Date Published2023 Feb 21
KeywordsGenome, Human, Genomics, High-Throughput Nucleotide Sequencing, Humans, Sequence Analysis, DNA

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.

Alternate JournalGenome Biol
PubMed ID36810122
PubMed Central IDPMC9942314
Grant ListDP2 MH119424 / MH / NIMH NIH HHS / United States
HHSN268201800002I / / NHLBI Division of Intramural Research /
1U01HG011758-01 / HG / NHGRI NIH HHS / United States
U01 AG058589 / AG / NIA NIH HHS / United States
DP2MH119424 / / National Institute of Mental Health and Neurosciences /
UM1HG008898 / HG / NHGRI NIH HHS / United States

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