/autocnv

Primary LanguageJupyter Notebook

AutoCNV: an Automatic Copy Number Variant Interpretation Tool

Installation

Pre-requirements

  • pysam: install pysam via conda:

    conda config --add channels r
conda config --add channels bioconda
conda install pysam

    For detail install instruction of pysam, please refer to the official document.

  • install autopvs1

  • install requirments pip install -r requirements.txt

Usage

please refer to the test cases.

Citation

@article{Fan2021,
    author = {Fan, Chunna and Wang, Zhonghua and Sun, Yan and Sun, Jun and Liu, Xi and Kang, Licheng and Xu, Yingshuo and Yang, Manqiu and Dai, Wentao and Song, Lijie and Wei, Xiaoming and Xiang, Jiale and Huang, Hui and Zhou, Meizhen and Zeng, Fanwei and Huang, Lin and Xu, Zhengfeng and Peng, Zhiyu},
    doi = {10.1186/s12864-021-08011-4},
    isbn = {1286402108011},
    issn = {14712164},
    journal = {BMC Genomics},
    keywords = {AutoCNV,CNV classification,CNV interpretation,Scoring},
    number = {1},
    pages = {1--12},
    pmid = {34615484},
    publisher = {BMC Genomics},
    title = {{AutoCNV: a semiautomatic CNV interpretation system based on the 2019 ACMG/ClinGen Technical Standards for CNVs}},
    volume = {22},
    year = {2021}
}