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 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) a

SUBMITTER: Pereira GS 

PROVIDER: S-EPMC6211426 | biostudies-literature | 2018 Nov

REPOSITORIES: biostudies-literature