Journal Article

High quality SNP calling using Illumina data at shallow coverage

Nawar Malhis and Steven J. M. Jones

in Bioinformatics

Volume 26, issue 8, pages 1029-1035
Published in print April 2010 | ISSN: 1367-4803
Published online February 2010 | e-ISSN: 1460-2059 | DOI:
High quality SNP calling using Illumina data at shallow coverage

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Motivation: Detection of single nucleotide polymorphisms (SNPs) has been a major application in processing second generation sequencing (SGS) data. In principle, SNPs are called on single base differences between a reference genome and a sequence generated from SGS short reads of a sample genome. However, this exercise is far from trivial; several parameters related to sequencing quality, and/or reference genome properties, play essential effect on the accuracy of called SNPs especially at shallow coverage data. In this work, we present Slider II, an alignment and SNP calling approach that demonstrates improved algorithmic approaches enabling larger number of called SNPs with lower false positive rate. In addition to the regular alignment and SNP calling, as an optional feature, Slider II is capable of utilizing information about known SNPs of a target genome, as priors, in the alignment and SNPs calling to enhance it's capability of detecting these known SNPs and novel SNPs and mutations in their vicinity.


Supplementary information and availability: Supplementary data are available at Bioinformatics online and at

Journal Article.  6048 words.  Illustrated.

Subjects: Bioinformatics and Computational Biology

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