A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids
Abstract Background Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heteroz...
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Bioinformatics |
| Subjects: | |
| Online Access: | http://link.springer.com/article/10.1186/s12859-018-2433-6 |
| _version_ | 1818544464995549184 |
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| author | Guilherme S. Pereira Antonio Augusto F. Garcia Gabriel R. A. Margarido |
| author_facet | Guilherme S. Pereira Antonio Augusto F. Garcia Gabriel R. A. Margarido |
| author_sort | Guilherme S. Pereira |
| collection | DOAJ |
| description | Abstract Background Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage. Results VCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SuperMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the Tassel-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species. Conclusions We demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data. |
| first_indexed | 2024-12-11T22:48:50Z |
| format | Article |
| id | doaj.art-e674f87963e046d2a5f56c95d5007bee |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-11T22:48:50Z |
| publishDate | 2018-11-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-e674f87963e046d2a5f56c95d5007bee2022-12-22T00:47:32ZengBMCBMC Bioinformatics1471-21052018-11-0119111010.1186/s12859-018-2433-6A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploidsGuilherme S. Pereira0Antonio Augusto F. Garcia1Gabriel R. A. Margarido2University of São Paulo, “Luiz de Queiroz” College of Agriculture, Department of GeneticsUniversity of São Paulo, “Luiz de Queiroz” College of Agriculture, Department of GeneticsUniversity of São Paulo, “Luiz de Queiroz” College of Agriculture, Department of GeneticsAbstract Background Genotyping-by-sequencing (GBS) has been used broadly in genetic studies for several species, especially those with agricultural importance. However, its use is still limited in autopolyploid species because genotype calling software generally fails to properly distinguish heterozygous classes based on allele dosage. Results VCF2SM is a Python script that integrates sequencing depth information of polymorphisms in variant call format (VCF) files and SuperMASSA software for quantitative genotype calling. VCFs can be obtained from any variant discovery software that outputs exact allele sequencing depth, such as a modified version of the Tassel-GBS pipeline provided here. VCF2SM was successfully applied in analyzing GBS data from diverse panels (alfalfa and potato) and full-sib mapping populations (alfalfa and switchgrass) of polyploid species. Conclusions We demonstrate that our approach can help plant geneticists working with autopolyploid species to advance their studies by distinguishing allele dosage from GBS data.http://link.springer.com/article/10.1186/s12859-018-2433-6Genotyping-by-sequencingPloidy estimationAllele dosagePopulation structureLinkage mappingGWAS |
| spellingShingle | Guilherme S. Pereira Antonio Augusto F. Garcia Gabriel R. A. Margarido A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids BMC Bioinformatics Genotyping-by-sequencing Ploidy estimation Allele dosage Population structure Linkage mapping GWAS |
| title | A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| title_full | A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| title_fullStr | A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| title_full_unstemmed | A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| title_short | A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| title_sort | fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids |
| topic | Genotyping-by-sequencing Ploidy estimation Allele dosage Population structure Linkage mapping GWAS |
| url | http://link.springer.com/article/10.1186/s12859-018-2433-6 |
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