popSTR2

popSTR2 performs microsatellite genotyping and detects pathogenic repeat expansions across samples to support population-scale and clinical analyses by estimating sample-specific slippage rates, joint-genotyping cohorts, and producing binned genotype outputs compatible with association pipelines.

Key Features:

• Sample-Specific Slippage Rate Estimation: Implements a kernel to estimate sample-specific slippage rates to improve detection of inter-sample microsatellite differences.
• Pathogenic Expansion Detection: Includes a curated panel of known pathogenic repeat expansions and a script that scans markers to flag potential pathogenic expansions for manual inspection.
• Joint Genotyping at Population Scale: Performs joint genotyping across multiple samples to enable population-scale microsatellite analysis.
• Binning Method for Enhanced Analysis: Transforms microsatellite genotypes into binned representations compatible with standard genetic association pipelines.

Scientific Applications:

• Population genetics: Genotyping microsatellites across cohorts to study allele frequency distributions and population variation.
• Clinical diagnostics: Screening and flagging of known pathogenic repeat expansions for downstream manual evaluation.
• Genomic epidemiology: Characterizing microsatellite variation across populations for epidemiological and diversity studies.
• Genetic association studies: Enabling association testing by providing binned genotype representations compatible with standard pipelines.

Methodology:

Processes sequencing data; applies a kernel to estimate sample-specific slippage rates; uses a curated pathogenic repeat panel and a scanning script to flag expansions; performs joint genotyping across samples; and applies a binning transformation to genotypes for compatibility with association pipelines.