A fully automated pipeline for quantitative genotype calling from next generation sequencing data in autopolyploids

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. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12859-018-2433-6) contains supplementary material, which is available to authorized users.