Improving SNP discovery by base alignment quality.
basic_science · Level V
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- Record sourced from PubMed, PMID 21320865.
- Also identified by DOI 10.1093/bioinformatics/btr076 and PMC identifier 3072548.
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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. http://samtools.sourceforge.net hengli@broadinstitute.org.
Medical subject headings
- Polymorphism, Single Nucleotide
- Sequence Alignment