cutehap 1.0.1

Haplotype-resolved genomic structural variation detection with cuteHap

cuteHap

A haplotype-resolved SV detector in phased long read sequencing data.

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Installation

We recommand the installation via conda or pip:

    $ conda install -c bioconda cutehap
	or
	$ pip install cutehap

Alternatively, installing from source with:

    git clone https://github.com/Meltpinkg/cuteHap.git
    cd cuteHap
    CFLAGS="-std=c99" python setup.py install

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Introduction

Structural variations (SVs), as a major category of genomic rearrangements, are capable of altering millions of nucleotides within the human genome. The detection of germline SVs and somatic mosaicism has emerged as a critical frontier in genomic research. Long-read sequencing technologies have demonstrated transformative potential in characterizing these variants. cuteHap is designed to produce high-quality, phased call sets for germline SV detection while simultaneously identifying low-frequency somatic mosaic events. The method delivers high-performance, haplotype-resolved SV detection and comprehensive detection of low-frequency mosaicism. A detailed usage guide documentation is available at here.

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Dependence

1. python3
2. scipy
2. pysam
3. Biopython
4. cigar
5. numpy
6. Cython

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Quick Start

cuteHap <phased.bam> <reference.fa> <output.vcf> <workdir>

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Changelog

cuteHap (v1.0.1)
1. update README.md
2. add user guide documentation
3. remove unused codes

cuteHap (v1.0.0)
1. the initial version of cuteHap

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Contact

For advising, bug reporting and requiring help, please post on Github Issue or contact [e-mail].