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Bioinformatics (Oxford, England) DOI:10.1093/bioinformatics/btr076

Improving SNP discovery by base alignment quality.

Publication TypeJournal Article
Year of Publication2011
AuthorsLi, H
JournalBioinformatics (Oxford, England)
Volume27
Issue8
Pages1157-8
Date Published2011/04/15
ISSN1367-4803
Abstract

I propose a new application of profile Hidden Markov Models 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, which accurately measures the probability of a read base being wrongly aligned. The effectiveness of BAQ has been positively confirmed on large datasets by the 1000 Genomes Project analysis subgroup. AVAILABILITY: http://samtools.sourceforge.net CONTACT: hengli@broadinstitute.org.

URLhttp://bioinformatics.oxfordjournals.org/cgi/pmidlookup?view=long&pmid=21320865
DOI10.1093/bioinformatics/btr076
Pubmed

http://www.ncbi.nlm.nih.gov/pubmed/21320865?dopt=Abstract