-
pysam: installpysamvia 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 -
install autocnv
python setup.py install --prefix $soft -
install database
ipython create-datebase.ipynb
please refer to the test cases.
- try test_annotation in
ipython test.ipynb
@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}
}