HaploPrep

This release provides the first public version of HaploPrep. This app identifies high-quality heterozygous SNPs (Single Nucleotide Polymorphisms) and prepares them for haplotype phasing by filtering variants based on population frequency, allelic balance, and sequencing depth from DNA-seq data.

HaploPrep includes utilities for organizing, filtering, and formatting genomic data used in downstream somatic mutation and haplotype analyses. The software facilitates standardized preparation of input files and intermediate data structures required by pipelines used to study clonal evolution and somatic mutation accumulation.

The toolkit is designed to integrate with other analysis workflows developed in the Shain Lab, including pipelines for single-cell–derived sequencing datasets and somatic mutation calling.

This release represents the initial public version of the HaploPrep codebase used in internal analysis workflows.

License: MIT License

Please cite the Zenodo DOI associated with this release when using this software in publications.

Changes in v1.0.0:

• Initial public release of HaploPrep
• Utilities for preparing genomic data for haplotype and somatic mutation analyses
• Documentation and example usage included in the repository