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

Abstract excerpt

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....

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