LinkImputeR: user-guided genotype calling and imputation for non-model organisms
Abstract Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation...
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| Format: | Article |
| Language: | English |
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BMC
2017-07-01
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| Series: | BMC Genomics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12864-017-3873-5 |
| _version_ | 1818953465488998400 |
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| author | Daniel Money Zoë Migicovsky Kyle Gardner Sean Myles |
| author_facet | Daniel Money Zoë Migicovsky Kyle Gardner Sean Myles |
| author_sort | Daniel Money |
| collection | DOAJ |
| description | Abstract Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Results Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. Conclusions By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from NGS technologies. It enables the user to quickly and easily examine the effects of varying thresholds and filters on the number and quality of the resulting genotype calls. In this manner, users can decide on thresholds that are most suitable for their purposes. We show that LinkImputeR can significantly augment the value and utility of NGS data sets, especially in non-model organisms with poor genomic resources. |
| first_indexed | 2024-12-20T10:06:42Z |
| format | Article |
| id | doaj.art-6abb05f18b194aeba858554a1b53037e |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-20T10:06:42Z |
| publishDate | 2017-07-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-6abb05f18b194aeba858554a1b53037e2022-12-21T19:44:13ZengBMCBMC Genomics1471-21642017-07-0118111210.1186/s12864-017-3873-5LinkImputeR: user-guided genotype calling and imputation for non-model organismsDaniel Money0Zoë Migicovsky1Kyle Gardner2Sean Myles3Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie UniversityDepartment of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie UniversityDepartment of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie UniversityDepartment of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie UniversityAbstract Background Genomic studies such as genome-wide association and genomic selection require genome-wide genotype data. All existing technologies used to create these data result in missing genotypes, which are often then inferred using genotype imputation software. However, existing imputation methods most often make use only of genotypes that are successfully inferred after having passed a certain read depth threshold. Because of this, any read information for genotypes that did not pass the threshold, and were thus set to missing, is ignored. Most genomic studies also choose read depth thresholds and quality filters without investigating their effects on the size and quality of the resulting genotype data. Moreover, almost all genotype imputation methods require ordered markers and are therefore of limited utility in non-model organisms. Results Here we introduce LinkImputeR, a software program that exploits the read count information that is normally ignored, and makes use of all available DNA sequence information for the purposes of genotype calling and imputation. It is specifically designed for non-model organisms since it requires neither ordered markers nor a reference panel of genotypes. Using next-generation DNA sequence (NGS) data from apple, cannabis and grape, we quantify the effect of varying read count and missingness thresholds on the quantity and quality of genotypes generated from LinkImputeR. We demonstrate that LinkImputeR can increase the number of genotype calls by more than an order of magnitude, can improve genotyping accuracy by several percent and can thus improve the power of downstream analyses. Moreover, we show that the effects of quality and read depth filters can differ substantially between data sets and should therefore be investigated on a per-study basis. Conclusions By exploiting DNA sequence data that is normally ignored during genotype calling and imputation, LinkImputeR can significantly improve both the quantity and quality of genotype data generated from NGS technologies. It enables the user to quickly and easily examine the effects of varying thresholds and filters on the number and quality of the resulting genotype calls. In this manner, users can decide on thresholds that are most suitable for their purposes. We show that LinkImputeR can significantly augment the value and utility of NGS data sets, especially in non-model organisms with poor genomic resources.http://link.springer.com/article/10.1186/s12864-017-3873-5ImputationGBSSNPRead count |
| spellingShingle | Daniel Money Zoë Migicovsky Kyle Gardner Sean Myles LinkImputeR: user-guided genotype calling and imputation for non-model organisms BMC Genomics Imputation GBS SNP Read count |
| title | LinkImputeR: user-guided genotype calling and imputation for non-model organisms |
| title_full | LinkImputeR: user-guided genotype calling and imputation for non-model organisms |
| title_fullStr | LinkImputeR: user-guided genotype calling and imputation for non-model organisms |
| title_full_unstemmed | LinkImputeR: user-guided genotype calling and imputation for non-model organisms |
| title_short | LinkImputeR: user-guided genotype calling and imputation for non-model organisms |
| title_sort | linkimputer user guided genotype calling and imputation for non model organisms |
| topic | Imputation GBS SNP Read count |
| url | http://link.springer.com/article/10.1186/s12864-017-3873-5 |
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