popSTR: population-scale detection of STR variants

Area of Science:

• Genomics
• Bioinformatics

Background:

• Microsatellites, or short tandem repeats (STRs), are abundant human genome variations.
• Their analysis is crucial for medical genetics, forensics, and genetic genealogy.
• Existing whole-genome sequencing studies often overlook microsatellites due to a lack of effective analytical tools.

Purpose of the Study:

• To present a novel microsatellite genotyper optimized for Illumina whole-genome sequencing (WGS) data.
• To offer a solution that is both faster and more accurate than existing methods for microsatellite analysis.

Main Methods:

• Utilizing pre-aligned sequencing data to minimize the amount of data required for microsatellite profiling.
• Implementing population information to train individual-specific error profiles for improved genotyping accuracy.

Main Results:

• The developed genotyper demonstrates superior speed and accuracy compared to previous methods.
• Achieved a 50% reduction in error rates when compared to lobSTR, a specialized microsatellite genotyping program.
• Genotyping results were validated against capillary electrophoresis data.

Conclusions:

• The new microsatellite genotyper significantly advances the analysis of STRs in WGS data.
• This tool enhances the utility of WGS for applications relying on microsatellite variation.
• The software is publicly available on GitHub for broader research use.