Using false discovery rates to benchmark SNP-callers in next-generation sequencing projects.

ABSTRACT: Sequence alignments form the basis for many comparative and population genomic studies. Alignment tools provide a range of accuracies dependent on the divergence between the sequences and the alignment methods. Despite widespread use, there is no standard method for assessing the accuracy of a dataset and alignment strategy after resequencing. We present a framework and tool for determining the overall accuracies of an input read dataset, alignment and SNP-calling method providing an isolate in that dataset has a corresponding, or closely related reference sequence available. In addition to this tool for comparing False Discovery Rates (FDR), we include a method for determining homozygous and heterozygous positions from an alignment using binomial probabilities for an expected error rate.

SUBMITTER: Farrer RA 

PROVIDER: S-EPMC3604800 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature