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Snagger: A user-friendly program for incorporating additional information for tagSNP selection
BACKGROUND: There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375134/ https://www.ncbi.nlm.nih.gov/pubmed/18371222 http://dx.doi.org/10.1186/1471-2105-9-174 |
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author | Edlund, Christopher K Lee, Won H Li, Dalin Van Den Berg, David J Conti, David V |
author_facet | Edlund, Christopher K Lee, Won H Li, Dalin Van Den Berg, David J Conti, David V |
author_sort | Edlund, Christopher K |
collection | PubMed |
description | BACKGROUND: There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important. RESULTS: We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r(2 )linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success, and (4) picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data. Using HapMap genotype data from ten ENCODE regions and design scores for the Illumina platform, we show similar coverage and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger. CONCLUSION: Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics. |
format | Text |
id | pubmed-2375134 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-23751342008-05-09 Snagger: A user-friendly program for incorporating additional information for tagSNP selection Edlund, Christopher K Lee, Won H Li, Dalin Van Den Berg, David J Conti, David V BMC Bioinformatics Software BACKGROUND: There has been considerable effort focused on developing efficient programs for tagging single-nucleotide polymorphisms (SNPs). Many of these programs do not account for potential reduced genomic coverage resulting from genotyping failures nor do they preferentially select SNPs based on functionality, which may be more likely to be biologically important. RESULTS: We have developed a user-friendly and efficient software program, Snagger, as an extension to the existing open-source software, Haploview, which uses pairwise r(2 )linkage disequilibrium between single nucleotide polymorphisms (SNPs) to select tagSNPs. Snagger distinguishes itself from existing SNP selection algorithms, including Tagger, by providing user options that allow for: (1) prioritization of tagSNPs based on certain characteristics, including platform-specific design scores, functionality (i.e., coding status), and chromosomal position, (2) efficient selection of SNPs across multiple populations, (3) selection of tagSNPs outside defined genomic regions to improve coverage and genotyping success, and (4) picking of surrogate tagSNPs that serve as backups for tagSNPs whose failure would result in a significant loss of data. Using HapMap genotype data from ten ENCODE regions and design scores for the Illumina platform, we show similar coverage and design score distribution and fewer total tagSNPs selected by Snagger compared to the web server Tagger. CONCLUSION: Snagger improves upon current available tagSNP software packages by providing a means for researchers to select tagSNPs that reliably capture genetic variation across multiple populations while accounting for significant genotyping failure risk and prioritizing on SNP-specific characteristics. BioMed Central 2008-03-27 /pmc/articles/PMC2375134/ /pubmed/18371222 http://dx.doi.org/10.1186/1471-2105-9-174 Text en Copyright © 2008 Edlund et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Edlund, Christopher K Lee, Won H Li, Dalin Van Den Berg, David J Conti, David V Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title | Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title_full | Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title_fullStr | Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title_full_unstemmed | Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title_short | Snagger: A user-friendly program for incorporating additional information for tagSNP selection |
title_sort | snagger: a user-friendly program for incorporating additional information for tagsnp selection |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375134/ https://www.ncbi.nlm.nih.gov/pubmed/18371222 http://dx.doi.org/10.1186/1471-2105-9-174 |
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