HipSTR

HipSTR is a software tool designed for accurate and efficient detection of genetic variants, specifically single nucleotide polymorphisms (SNPs) and short insertions and deletions (indels), in next-generation sequencing data. It is particularly well-suited for analyzing low-frequency variants, which are often challenging to identify reliably due to sequencing errors. HipSTR stands for "High-fidelity Insertion/Deletion STR" and emphasizes its capability in accurately calling both SNPs and indels, especially in repetitive regions where traditional methods may struggle.

The tool employs a statistical model that considers the read depth, base quality scores, and mapping quality to distinguish true variants from sequencing noise. It models the genotype likelihoods based on an expectation-maximization algorithm, allowing for robust variant calling even with limited coverage. HipSTR is designed to be computationally efficient, enabling its use on large datasets. It supports various sequencing data formats, such as BAM files, and outputs variant calls in standard formats like VCF (Variant Call Format). Its ability to handle repetitive regions and low-frequency variants makes it valuable for applications in population genetics, cancer research, and the study of complex diseases where subtle genetic variations can have significant functional implications.