Affordable Access

deepdyve-link deepdyve-link
Publisher Website

SNPest: a probabilistic graphical model for estimating genotypes.

Authors
  • Lindgreen, Stinus
  • Krogh, Anders
  • Pedersen, Jakob Skou
Type
Published Article
Journal
BMC Research Notes
Publisher
Springer (Biomed Central Ltd.)
Publication Date
Jan 01, 2014
Volume
7
Pages
698–698
Identifiers
DOI: 10.1186/1756-0500-7-698
PMID: 25294605
Source
Medline
License
Unknown

Abstract

We compare the performance of SNPest to a number of other widely used genotypers on both real and simulated data, covering both haploid and diploid genomes. We investigate the effects of read depth, of removing adapters before mapping and genotyping, of using different mapping tools, and of using the correct model in the genotyping process. We show that the performance of SNPest is comparable to existing methods, and we also illustrate cases where SNPest has an advantage over other methods, e.g. when dealing with simulated ancient DNA.

Report this publication

Statistics

Seen <100 times