cutehap 1.0.0

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:

    The installation via conda and pypi is now in construction.

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

cuteHap detects germline or mosaic structural variations (SVs) through phased long reads sequencing alignments.

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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 (v1.0.0)
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].