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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Published in:Genome Biology Vol. 24; no. 1; p. 31
Main Authors: 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.
Format: Journal Article
Language:English
Published: London BioMed Central 21.02.2023
Springer Nature B.V
BMC
Subjects:
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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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.
AbstractList 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.
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.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.
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.
ArticleNumber 31
Author Orchard, Peter
Sedlazeck, Fritz J.
Mahmoud, Medhat
LeFaive, Jonathon
Dennis, Megan Y.
Farek, Jesse
Soto, Daniela C.
Behera, Sairam
Paulin, Luis F.
Parker, Stephen C. J.
Smith, Albert V.
Zook, Justin M.
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Issue 1
Keywords Variant
GIAB
T2T-CHM13
Remapping
Reference
SNV
eQTL
Medically relevant genes
GRCh38
INDEL
Language English
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Snippet 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...
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...
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SubjectTerms 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
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Title FixItFelix: improving genomic analysis by fixing reference errors
URI https://link.springer.com/article/10.1186/s13059-023-02863-7
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