Journal
GENOME BIOLOGY
Volume 22, Issue 1, Pages -Publisher
BMC
DOI: 10.1186/s13059-021-02474-0
Keywords
Genome graph; Pangenome; Variant calling; Plasmodium falciparum; Mycobacterium tuberculosis; VCF
Funding
- Wellcome Trust/Newton Fund-MRC Collaborative Award [200205]
- Bill & Melinda Gates Foundation Trust [OPP1133541]
- Projekt DEAL
- EMBL predoctoral fellowship
- Bill and Melinda Gates Foundation [OPP1133541] Funding Source: Bill and Melinda Gates Foundation
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Genome graphs provide a general way to represent genetic variation, allowing for multiscale variation and transparency on different sequence backgrounds. The software gramtools can handle variant calls on multiple references and outperforms existing methods in genotyping SNPs overlapping large deletions.
Genome graphs allow very general representations of genetic variation; depending on the model and implementation, variation at different length-scales (single nucleotide polymorphisms (SNPs), structural variants) and on different sequence backgrounds can be incorporated with different levels of transparency. We implement a model which handles this multiscale variation and develop a JSON extension of VCF (jVCF) allowing for variant calls on multiple references, both implemented in our software gramtools. We find gramtools outperforms existing methods for genotyping SNPs overlapping large deletions in M. tuberculosis and is able to genotype on multiple alternate backgrounds in P. falciparum, revealing previously hidden recombination.
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