Efficient selective screening of haplotype tag SNPs.
Haplotypes defined by common single nucleotide polymorphisms (SNPs) have important implications for mapping of disease genes and human traits. Often only a small subset of the SNPs is sufficient to capture the full haplotype information. Such subsets of markers are called haplotype tagging SNPs (htSNPs). Although htSNPs can be identified by eye, efficient computer algorithms and flexible interactive software tools are required for large datasets such as the human genome haplotype map. We describe a java-based program, SNPtagger, which screens for minimal sets of SNP markers to represent given haplotypes according to various user requirements. The program offers several options for inclusion/exclusion of specific markers and presents alternative panels for final selection.


BACKGROUND
The www-based program is available at http://www.well.ox.ac.uk/~xiayi/haplotype/index.html.
Ke
Xiayi
X
Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. xiayi@well.ox.ac.uk
Cardon
Lon R
LR
D000465:Algorithms; D001483:Base Sequence; D030541:Databases, Genetic; D005787:Gene Frequency / Q000235:genetics; D005819:Genetic Markers / Q000235:genetics; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide; D011786:Quality Control; D012689:Sequence Homology, Nucleic Acid; D014584:User-Computer Interface
D005819:Genetic Markers