⚠️ This repository is obsolete — Do not use

BaseVar1 is no longer maintained. Please use BaseVar2.

🌐 New repository & docs: https://github.com/ShujiaHuang/BaseVar2

Introduction

BaseVar is a specialized tool for variant calling from ultra low-depth (<1x) sequencing data, with particular focus on non-invasive prenatal testing (NIPT) and large-scale population genomics. Leveraging maximum likelihood and likelihood ratio models, BaseVar accurately identifies polymorphisms at genomic positions and estimates allele frequencies across thousands of samples simultaneously. For the mathematical foundations, refer to the BaseVar publication in Cell Genomics.