Artificial intelligence in variant calling: a review
Artificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis. Variant calling involves the detection of genetic variants such as single nucleotide polymorphisms (SNPs), insertions/delet...
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2025-04-01
|
| Series: | Frontiers in Bioinformatics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1574359/full |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850200958225612800 |
|---|---|
| author | Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh |
| author_facet | Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh |
| author_sort | Omar Abdelwahab |
| collection | DOAJ |
| description | Artificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis. Variant calling involves the detection of genetic variants such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variants from high-throughput sequencing data. Traditionally, statistical approaches have dominated this task, but the advent of AI led to the development of sophisticated tools that promise higher accuracy, efficiency, and scalability. This review explores the state-of-the-art AI-based variant calling tools, including DeepVariant, DNAscope, DeepTrio, Clair, Clairvoyante, Medaka, and HELLO. We discuss their underlying methodologies, strengths, limitations, and performance metrics across different sequencing technologies, alongside their computational requirements, focusing primarily on SNP and InDel detection. By comparing these AI-driven techniques with conventional methods, we highlight the transformative advancements AI has introduced and its potential to further enhance genomic research. |
| format | Article |
| id | doaj-art-2112bef1c7cb42ea9d6f2c2c29a3e266 |
| institution | OA Journals |
| issn | 2673-7647 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Bioinformatics |
| spelling | doaj-art-2112bef1c7cb42ea9d6f2c2c29a3e2662025-08-20T02:12:10ZengFrontiers Media S.A.Frontiers in Bioinformatics2673-76472025-04-01510.3389/fbinf.2025.15743591574359Artificial intelligence in variant calling: a reviewOmar Abdelwahab0Omar Abdelwahab1Omar Abdelwahab2Omar Abdelwahab3Davoud Torkamaneh4Davoud Torkamaneh5Davoud Torkamaneh6Davoud Torkamaneh7Département de Phytologie, Université Laval, Québec City, QC, CanadaInstitut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, CanadaCentre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, CanadaInstitut intelligence et données (IID), Université Laval, Québec City, QC, CanadaDépartement de Phytologie, Université Laval, Québec City, QC, CanadaInstitut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, CanadaCentre de recherche et d’innovation sur les végétaux (CRIV), Université Laval, Québec City, QC, CanadaInstitut intelligence et données (IID), Université Laval, Québec City, QC, CanadaArtificial intelligence (AI) has revolutionized numerous fields, including genomics, where it has significantly impacted variant calling, a crucial process in genomic analysis. Variant calling involves the detection of genetic variants such as single nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variants from high-throughput sequencing data. Traditionally, statistical approaches have dominated this task, but the advent of AI led to the development of sophisticated tools that promise higher accuracy, efficiency, and scalability. This review explores the state-of-the-art AI-based variant calling tools, including DeepVariant, DNAscope, DeepTrio, Clair, Clairvoyante, Medaka, and HELLO. We discuss their underlying methodologies, strengths, limitations, and performance metrics across different sequencing technologies, alongside their computational requirements, focusing primarily on SNP and InDel detection. By comparing these AI-driven techniques with conventional methods, we highlight the transformative advancements AI has introduced and its potential to further enhance genomic research.https://www.frontiersin.org/articles/10.3389/fbinf.2025.1574359/fullvariant callingartificial intelligencedeep learninggenomicsmachine learning (ML) |
| spellingShingle | Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Omar Abdelwahab Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh Davoud Torkamaneh Artificial intelligence in variant calling: a review Frontiers in Bioinformatics variant calling artificial intelligence deep learning genomics machine learning (ML) |
| title | Artificial intelligence in variant calling: a review |
| title_full | Artificial intelligence in variant calling: a review |
| title_fullStr | Artificial intelligence in variant calling: a review |
| title_full_unstemmed | Artificial intelligence in variant calling: a review |
| title_short | Artificial intelligence in variant calling: a review |
| title_sort | artificial intelligence in variant calling a review |
| topic | variant calling artificial intelligence deep learning genomics machine learning (ML) |
| url | https://www.frontiersin.org/articles/10.3389/fbinf.2025.1574359/full |
| work_keys_str_mv | AT omarabdelwahab artificialintelligenceinvariantcallingareview AT omarabdelwahab artificialintelligenceinvariantcallingareview AT omarabdelwahab artificialintelligenceinvariantcallingareview AT omarabdelwahab artificialintelligenceinvariantcallingareview AT davoudtorkamaneh artificialintelligenceinvariantcallingareview AT davoudtorkamaneh artificialintelligenceinvariantcallingareview AT davoudtorkamaneh artificialintelligenceinvariantcallingareview AT davoudtorkamaneh artificialintelligenceinvariantcallingareview |