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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Vydáno v:Genome Biology Ročník 24; číslo 1; s. 31
Hlavní autoři: 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.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London BioMed Central 21.02.2023
Springer Nature B.V
BMC
Témata:
Animal Genetics and Genomics
Bioinformatics
Biomedical and Life Sciences
Evolutionary Biology
genome
Genome, Human
Genomes
Genomic analysis
Genomics
GRCh38
High-Throughput Nucleotide Sequencing
Human Genetics
Humans
INDEL
Life Sciences
Method
Microbial Genetics and Genomics
nationalities and ethnic groups
Plant Genetics and Genomics
Sequence Analysis, DNA
SNV
T2T-CHM13
Variant
Variant
GIAB
T2T-CHM13
Remapping
Reference
SNV
eQTL
Medically relevant genes
GRCh38
INDEL
ISSN:1474-760X, 1474-7596, 1474-760X
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Shrnutí: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.
Bibliografie:ObjectType-Article-1
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ISSN:1474-760X
1474-7596
1474-760X
DOI:10.1186/s13059-023-02863-7