PySmooth: a Python tool for the removal and correction of genotyping errors

Abstract

Abstract Summary In genetic mapping studies involving many individuals, genome-wide markers such as single nucleotide polymorphisms (SNPs) can be detected using different methods. However, it comes with some errors. Some SNPs associated with diseases can be in regions encoding long noncoding RNAs (lncRNAs). Therefore, identifying the errors in genotype file and correcting them is crucial for accurate genetic mapping studies. We develop a Python tool called PySmooth, that offers an easy-to-use command line interface for the removal and correction of genotyping errors. PySmooth uses the approach of a previous tool called SMOOTH with some modifications. It inputs a genotype file, detects errors and corrects them. PySmooth provides additional features such as imputing missing data, better user-friendly usage, generates summary and visualization files, has flexible parameters, and handles more genotype codes. Availability and implementation PySmooth is available at https://github.com/lncRNAAddict/PySmooth .

Keywords

• SNPS
• QTLs
• SMOOTH
• genotype mapping and correction