The discovery and characterization of sequence variations in human populations are crucial in genetic studies. Standard methods for addressing this problem are computationally expensive and highly time-consuming, thus impractical for clinical applications, where time is often an issue. When the task is to genotype variations that have been previously annotated, alignment-free methods come to the aid. Here, we describe MALVA, an alignment-free approach for genotyping a set of known variations. MALVA is the first mapping-free tool which is able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variations.
Alignment-Free Genotyping of Known Variations with MALVA
Bernardini, Giulia;
2022-01-01
Abstract
The discovery and characterization of sequence variations in human populations are crucial in genetic studies. Standard methods for addressing this problem are computationally expensive and highly time-consuming, thus impractical for clinical applications, where time is often an issue. When the task is to genotype variations that have been previously annotated, alignment-free methods come to the aid. Here, we describe MALVA, an alignment-free approach for genotyping a set of known variations. MALVA is the first mapping-free tool which is able to genotype multi-allelic SNPs and indels, even in high-density genomic regions, and to effectively handle a huge number of variations.File | Dimensione | Formato | |
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(Methods in Molecular Biology, 2493) Charlotte Ng, Salvatore Piscuoglio - Variant Calling_ Methods and Protocols-Humana Press (2022)-2-1-19.pdf
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