Software for Quantifying and Simulating Microsatellite Genotyping Error
Microsatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2007-01-01
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| Series: | Bioinformatics and Biology Insights |
| Subjects: | |
| Online Access: | http://la-press.com/article.php?article_id=432 |
| _version_ | 1818456590443872256 |
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| author | Paul C.D. Johnson Daniel T. Haydon |
| author_facet | Paul C.D. Johnson Daniel T. Haydon |
| author_sort | Paul C.D. Johnson |
| collection | DOAJ |
| description | Microsatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit from separating errors into two distinct classes: allelic dropout and false alleles. Pedant is MS Windows software for estimating locus-specific maximum likelihood rates of these two classes of error. Estimation is based on comparison of duplicate error-prone genotypes: neither reference genotypes nor pedigree data are required. Other functions include: plotting of error rate estimates and confidence intervals; simulations for performing power analysis and for testing the robustness of error rate estimates to violation of the underlying assumptions; and estimation of expected heterozygosity, which is a required input. The program, documentation and source code are available from http://www.stats.gla.ac.uk/~paulj/pedant.html. |
| first_indexed | 2024-12-14T22:29:05Z |
| format | Article |
| id | doaj.art-35cc5f2b0a434b3fb885b0c14710b0d7 |
| institution | Directory Open Access Journal |
| issn | 1177-9322 |
| language | English |
| last_indexed | 2024-12-14T22:29:05Z |
| publishDate | 2007-01-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Bioinformatics and Biology Insights |
| spelling | doaj.art-35cc5f2b0a434b3fb885b0c14710b0d72022-12-21T22:45:16ZengSAGE PublishingBioinformatics and Biology Insights1177-93222007-01-0117175Software for Quantifying and Simulating Microsatellite Genotyping ErrorPaul C.D. JohnsonDaniel T. HaydonMicrosatellite genetic marker data are exploited in a variety of fields, including forensics, gene mapping, kinship inference and population genetics. In all of these fields, inference can be thwarted by failure to quantify and account for data errors, and kinship inference in particular can benefit from separating errors into two distinct classes: allelic dropout and false alleles. Pedant is MS Windows software for estimating locus-specific maximum likelihood rates of these two classes of error. Estimation is based on comparison of duplicate error-prone genotypes: neither reference genotypes nor pedigree data are required. Other functions include: plotting of error rate estimates and confidence intervals; simulations for performing power analysis and for testing the robustness of error rate estimates to violation of the underlying assumptions; and estimation of expected heterozygosity, which is a required input. The program, documentation and source code are available from http://www.stats.gla.ac.uk/~paulj/pedant.html.http://la-press.com/article.php?article_id=432microsatellitesgenotyping errorallelic dropoutfalse allelesmaximum likelihoodsoftware |
| spellingShingle | Paul C.D. Johnson Daniel T. Haydon Software for Quantifying and Simulating Microsatellite Genotyping Error Bioinformatics and Biology Insights microsatellites genotyping error allelic dropout false alleles maximum likelihood software |
| title | Software for Quantifying and Simulating Microsatellite Genotyping Error |
| title_full | Software for Quantifying and Simulating Microsatellite Genotyping Error |
| title_fullStr | Software for Quantifying and Simulating Microsatellite Genotyping Error |
| title_full_unstemmed | Software for Quantifying and Simulating Microsatellite Genotyping Error |
| title_short | Software for Quantifying and Simulating Microsatellite Genotyping Error |
| title_sort | software for quantifying and simulating microsatellite genotyping error |
| topic | microsatellites genotyping error allelic dropout false alleles maximum likelihood software |
| url | http://la-press.com/article.php?article_id=432 |
| work_keys_str_mv | AT paulcdjohnson softwareforquantifyingandsimulatingmicrosatellitegenotypingerror AT danielthaydon softwareforquantifyingandsimulatingmicrosatellitegenotypingerror |