PyroHMMvar: a sensitive and accurate method to call short indels and SNPs for Ion Torrent and 454 data.

ABSTRACT:

Motivation

The identification of short insertions and deletions (indels) and single nucleotide polymorphisms (SNPs) from Ion Torrent and 454 reads is a challenging problem, essentially because these techniques are prone to sequence erroneously at homopolymers and can, therefore, raise indels in reads. Most of the existing mapping programs do not model homopolymer errors when aligning reads against the reference. The resulting alignments will then contain various kinds of mismatches and indels that confound the accurate determination of variant loci and alleles.

Results

To address these challenges, we realign reads against the reference using our previously proposed hidden Markov model that models homopolymer errors and then merges these pairwise alignments into a weighted al

SUBMITTER: Zeng F 

PROVIDER: S-EPMC3888126 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature