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ShujiaHuang committed Dec 17, 2024
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*BaseVar* is a specialized tool tailored for variant calling using ultra low-depth (<1x) sequencing data, particularly catering to non-invasive prenatal test (NIPT) data in human genetic studies. Leveraging maximum likelihood and likelihood ratio models, BaseVar accurately identifies polymorphisms at genomic positions and calculates allele frequencies. For in-depth mathematical explanations, refer to the comprehensive documentation available [here](https://doi.org/10.1016/j.cell.2018.08.016).

Now, BaseVar has been fully implemented by C++. BaseVar showcases significant enhancements over its [original Python counterpart](https://github.com/ShujiaHuang/basevar/tree/python-version-0.6.1.1). The C++ implementation delivers a computing speed exceeding 20 times that of the Python version, all while demanding substantially less memory. Typically, each thread (-t/--thread) consumes merely 3GB to 4GB of memory when the -B (--batch-count) option is configured to 200, a stark contrast to the Python version's requirement of over 20GB.
Now, BaseVar has been fully implemented by C++. BaseVar showcases significant enhancements over its [original Python counterpart](https://github.com/ShujiaHuang/basevar/tree/python-version-0.6.1.1). The C++ implementation delivers a computing speed exceeding 10 times that of the Python version, all while demanding substantially less memory. Typically, each thread (-t/--thread) consumes merely 3GB to 4GB of memory when the -B (--batch-count) option is configured to 200, a stark contrast to the Python version's requirement of over 20GB.


## Citation
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BaseVar is hosted on Github and can be downloaded with the following command:
```bash
$ git clone --recursive https://github.com/ShujiaHuang/basevar.git
$ git clone https://github.com/ShujiaHuang/basevar.git
```
> **WARNING**: Please try several times if fail to clone the data causing by the network problem.
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