Fast genotyping of known SNPs through approximate k-mer matching.

ABSTRACT:

Motivation

As the volume of next-generation sequencing (NGS) data increases, faster algorithms become necessary. Although speeding up individual components of a sequence analysis pipeline (e.g. read mapping) can reduce the computational cost of analysis, such approaches do not take full advantage of the particulars of a given problem. One problem of great interest, genotyping a known set of variants (e.g. dbSNP or Affymetrix SNPs), is important for characterization of known genetic traits and causative disease variants within an individual, as well as the initial stage of many ancestral and population genomic pipelines (e.g. GWAS).

Results

We introduce lightweight assignment of variant alleles (LAVA), an NGS-based genotyping algorithm for a given set of SNP loci, which takes

SUBMITTER: Shajii A 

PROVIDER: S-EPMC5013917 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature