HiScanner (HIgh-resolution Single-Cell Allelic copy Number callER)

HiScanner is a lightweight python package for high-resolution single-cell copy number analysis.

Content

• Installation
• Requirements
• Quick Start
• Operating System
• Documentation
• Contributing
• Support
• LICENSE

Installation

It is recommended to install HiScanner in a virtual environment. Here's how to create one using conda:

conda create -n hiscanner_env python=3.8
conda activate hiscanner_env

To install HiScanner, simply use pip:

pip install hiscanner

Requirements

HiScanner requires bcftools, which must be included in PATH. All other dependencies should be installed automatically with pip.

Quick Start

To get started with HiScanner, please refer to our tutorial. Here's a quick example:

import hiscanner
# define your json file path
path = "your/dir/to/json"
# preprocess
hiscanner.pp.preprocess(path)
# segment
hiscanner.tl.segment(path)
# infer copy number
hiscanner.tl.infer_copy_number(path)
# visualize 
hiscanner.pl.plot_whole_genome_track(path)

Command line interface

For advanced users interested in multi-sample segmentation (e.g., repurposing for bulk samples), HiScanner provides a command line interface. In bash, simply run:

hiscanner-segment -i {input_file} -l {LAMBDA} -o {output_file}

For more details, please refer to our documentation.

Required input

1) JSON

HiScanner requires a json file as input. Here's an example:

{
    "bin_path": "/Users/yifan/dev/scanner_tutorial/tests/data/bins",
    "phase_file": "/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_phased_hsnps.vcf",
    "germline": "bulkname",
    "gatk_vcf": "/Users/yifan/dev/scanner_tutorial/tests/data/hsnps/samplename_gatk.vcf",
    "stem": "/Users/yifan/dev/scanner_tutorial/tests/data/output/",
    "j": 20,
    "singlecell":"cellA,cellB",
    "MAX_WGD": 1,
    "LAMBDA":200
}

2) BAM

The BAM file should be indexed and sorted.

3) Unphased VCF

output from GATK or SCAN-SNV; The VCF file should be indexed and sorted.

4) Phased VCF

output from Eagle or other phasing tools;

5) Bins

The bins file should be a bed file (output from BIC-seq2)

Operating System

HiScanner was tested in the following operating systems:

• macOS Ventura 13.5.2
• CentOS Linux 7.9
• Windows 11

Documentation

For more detailed information and advanced usage, please refer to our documentation.

Support

HiScanner is currently under active development. For support or questions, please open an issue on our GitHub repository.

Contributing

Contributions to HiScanner are welcome. Please refer to our contribution guidelines for more information.

LICENSE

HiScanner is released under the MIT License, and is freely available for non-commercial use.