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 in questo prodotto:
File Dimensione Formato  
(Methods in Molecular Biology, 2493) Charlotte Ng, Salvatore Piscuoglio - Variant Calling_ Methods and Protocols-Humana Press (2022)-2-1-19.pdf

Accesso chiuso

Tipologia: Documento in Versione Editoriale
Licenza: Copyright Editore
Dimensione 751.03 kB
Formato Adobe PDF
751.03 kB Adobe PDF   Visualizza/Apri   Richiedi una copia
(Methods+in+Molecular+Biology,+2493)+Charlotte+Ng,+Salvatore+Piscuoglio+-+Variant+Calling_+Methods+and+Protocols-Humana+Press+(2022)-2-1-19-Post_print.pdf

Open Access dal 27/06/2023

Tipologia: Bozza finale post-referaggio (post-print)
Licenza: Digital Rights Management non definito
Dimensione 757.73 kB
Formato Adobe PDF
757.73 kB Adobe PDF Visualizza/Apri
Pubblicazioni consigliate

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11368/3024841
Citazioni
  • ???jsp.display-item.citation.pmc??? 0
  • Scopus 0
  • ???jsp.display-item.citation.isi??? ND
social impact