Saturday, February 19, 2011

Improving SNP discovery by base alignment quality

Improving SNP discovery by base alignment quality:

Summary: I propose a new application of profile Hidden Markov Models (HMMs) in the area of SNP discovery from resequencing data, to greatly reduce false SNP calls caused by misalignments around insertions and deletions (indels). The central concept is per-Base Alignment Quality (BAQ) which accurately measures the probability of a read base being wrongly aligned. The effectiveness of BAQ has been positively confirmed on large data sets by the 1000 Genomes Project analysis subgroup.

Availability:http://samtools.sourceforge.net

Contact:hengli@broadinstitute.org


(Via Bioinformatics - Advance Access.)