ArticleGenome biology2023
FixItFelix: improving genomic analysis by fixing reference errors.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- An Icelandic pangenome reference.Nature · 2026Article
- T2T-CHM13 improves read mapping and detection of clinically relevant genetic variation in the Swedish population.Genome research · 2025Article
- GREGoR: accelerating genomics for rare diseases.Nature · 2025Article
- Read mismapping from segmental duplications drives spuriousbioRxiv : the preprint server for biology · 2025Article
- Article
- Accurate human genome analysis with element avidity sequencing.BMC bioinformatics · 2025Article
- Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.Scientific data · 2025Article
- Comprehensive genome analysis and variant detection at scale using DRAGEN.Nature biotechnology · 2025Article
- Development and extensive sequencing of a broadly-consented Genome in a Bottle matched tumor-normal pair.bioRxiv : the preprint server for biology · 2025Article
- Analytical validation of germline small variant detection using long-read HiFi genome sequencing.Genome research · 2025Article
- T2T-CHM13 versus hg38: accurate identification of immunoglobulin isotypes from scRNA-seq requires a genome reference matched for ancestry.NAR genomics and bioinformatics · 2025Article
- Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T.Genome research · 2025Article
- A Hitchhiker's Guide to long-read genomic analysis.Genome research · 2025Review
- Article
- GREGoR: Accelerating Genomics for Rare Diseases.ArXiv · 2024Article
- The GIAB genomic stratifications resource for human reference genomes.Nature communications · 2024Article
- Impact and characterization of serial structural variations across humans and great apes.Nature communications · 2024Article
- Impact of genome build on RNA-seq interpretation and diagnostics.American journal of human genetics · 2024Article
- Closing the gap: Solving complex medically relevant genes at scale.medRxiv : the preprint server for health sciences · 2024Article
- The benefit of a complete reference genome for cancer structural variant analysis.medRxiv : the preprint server for health sciences · 2024Article
Corrections and comments
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Authors and funding
12 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.