FixItFelix: improving genomic analysis by fixing reference errors
Open accessAbstract
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.
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The 12 medically important genes underrepresented on GRCh38 comprise 9 that are incorrectly duplicated and 3 that are incorrectly collapsed.
“These 12 genes comprise 9 that are incorrectly duplicated and 3 that are incorrectly collapsed (for example, two instead of three copies).”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
The Discussion says false duplications affected 12 medically relevant genes, rather than nine. The Results (Identification of GRCh38 errors) separately identify three medically relevant genes selected from collapsed regions; they do not describe those three as part of a 12-gene group split nine and three. Page numbers were not available in our copy. (LLM, conf=0.86)
Checked by a reasoning model — may be wrong.
Experimental — accuracy not yet measuredFor MAP2K3 and KCNJ18, GATK discovered 487 more variants than DRAGEN, which are likely false positives.
“For MAP2K3, which is related to skin and liver diseases67, and KCNJ18, which is related to other rare diseases68, GATK discovered 487 more variants than DRAGEN, which are likely false positives23 (Supplementary Table 11).”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
The Results (General improvements of variant calling; The modified reference improves variant detection across ancestries) report improved variant-call accuracy in regions containing MAP2K3 and KCNJ18, consistent with erroneous calls in those regions. But the paper compares GATK calls before and after reference modification, not GATK with DRAGEN; it does not substantiate the figure of 487 additional variants or identify those particular variants as likely false positives. (LLM, conf=0.87)
Experimental — accuracy not yet measuredSeveral medically relevant genes are wrongly represented in the GRCh38 reference due to false duplication and collapsed sequence errors.
“Moreover, several of these medically relevant genes (for example, KCNE1, CBS, CRYAA, KCNJ18, MAP2K3, KMT2C) are wrongly represented in the GRCh38 reference due to false duplication and collapsed sequence errors23.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
Several genes have been wrongly reported multiple times across the genome, which often leads to missing variant calls due to their repetitiveness.
“On the other hand, there are several genes that have been wrongly reported multiple times across the genome, which often leads to missing variant calls due to their repetitiveness23.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
Within medically relevant genes, there are 12 genes that are often negatively impacted by reference bias.
“Within these medically relevant genes, there are 12 genes that are often negatively impacted by reference bias23.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
Some genes suffer from wrongly collapsed copies, which leads to an increased number of variants.
“As mentioned before, some genes suffer from wrongly collapsed copies, which leads to an increased number of variants23.”
From Comprehensive genome analysis and variant detection at scale using DRAGEN (2025) · cites this paper as [23]
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Additional file 1 of Genomic variant benchmark: if you cannot measure it, you cannot improve it
Majidian, S., Agustinho, D. P., Chin, C.-S., Sedlazeck, F. J., & Mahmoud, M. (2023) · Figshare · doi:10.6084/m9.figshare.24257470
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Self-citationRondot, F., Centofanti, F., Micaletto, A., Angheben, L., Fontana, F., Rossi, N., Cerrato, F., Pignata, L., Carta, G., Tommaso, S. D., et al. (2026) · Scientific Reports · doi:10.1038/s41598-026-59431-9
An Icelandic pangenome reference
Holley, G., Eggertsson, H. P., Kristmundsdóttir, S., Beyter, D., Skúladóttir, Á., Moore, K. H. S., Olason, P. I., Gylfason, A., Magnusson, O. T., Oddsson, Á., et al. (2026) · Nature · doi:10.1038/s41586-026-10924-7
Bioinformatics for human long-read whole-genome sequencing
Zheng, X., Sanio, P., Luo, R., Li, H., & Sedlazeck, F. J. (2026) · Nature Reviews Methods Primers · doi:10.1038/s43586-026-00519-x · Cited by 1 · see citing works
Self-citationSmall variant calling in the era of long-read sequencing
Zheng, Z., Sedlazeck, F. J., & Luo, R. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-026-01020-7
Self-citation
- Authors
- Behera, S., LeFaive, J., Orchard, P., Mahmoud, M., Paulin, L. F., Farek, J., Soto, D. C., Parker, S. C. J., Smith, A. V., Dennis, M. Y., Zook, J. M., & Sedlazeck, F. J.
- Affiliations
- Baylor College of Medicine (US)
- University of Michigan (US)
- University of California, Davis (US)
- National Institute of Standards and Technology (US)
- Corresponding author
- Zook, Justin M.
- Sedlazeck, Fritz J.
- ORCID
- Venue
- Genome Biology
- Published
- 2023-02-21
- Volume
- 24
- Issue
- 1
- Pages
- 31-31
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- PMC
- PMC9942314
- OpenAlex
- W4321460043
- Cited by
- 28
- References
- 43
- Citations by year
- 2026: 5 · 2025: 10 · 2024: 9 · 2023: 4
- FWCI
- 2.50
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genome biology (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- eScholarship (California Digital Library) (submittedVersion, cc-by)
- Digital Commons-TMC (Texas Medical Center) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Rice Research Repository (Rice University) (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute (UM1HG008898, 1U01HG011758-01)
- NHLBI Division of Intramural Research (HHSN268201800002I)
- National Institute on Aging (U01 AG058589)
- National Institute of Mental Health and Neurosciences (DP2MH119424)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- GRCh38, remapping, variant calling, protein-coding genes, expression quantitative trait loci, human genome
- MeSH terms
- Humans, Genome, Human, Sequence Analysis, DNA, Genomics, High-Throughput Nucleotide Sequencing
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