Reference-free SNP calling: improved accuracy by preventing incorrect calls from repetitive genomic regions.

ABSTRACT:

Background

Single nucleotide polymorphisms (SNPs) are the most abundant type of genetic variation in eukaryotic genomes and have recently become the marker of choice in a wide variety of ecological and evolutionary studies. The advent of next-generation sequencing (NGS) technologies has made it possible to efficiently genotype a large number of SNPs in the non-model organisms with no or limited genomic resources. Most NGS-based genotyping methods require a reference genome to perform accurate SNP calling. Little effort, however, has yet been devoted to developing or improving algorithms for accurate SNP calling in the absence of a reference genome.

Results

Here we describe an improved maximum likelihood (ML) algorithm called iML, which can achieve high genotyping accuracy fo

SUBMITTER: Dou J 

PROVIDER: S-EPMC3472322 | biostudies-literature | 2012 Jun

REPOSITORIES: biostudies-literature