Metadata-Version: 1.2
Name: basevar
Version: 0.0.1.2
Summary: BaseVar: A python software for calling variants from ultra low pass WGS data.
Home-page: https://git.bgionline.cn/huangshujia/BaseVar
Author: Shujia Huang & Siyang Liu
Author-email: huangshujia9@gmail.com
Maintainer: Shujia Huang & Siyang Liu
Maintainer-email: huangshujia9@gmail.com
License: BSD (3-clause)
Download-URL: https://git.bgionline.cn/huangshujia/BaseVar
Description: BaseVar
        =======
        
        Call variants from ultra low-pass WGS data.
        
        Installation
        ------------
        
        .. code:: bash
        
        
            pip install basevar
        
        Quick start
        -----------
        
        Call variants from several bamfiles
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
            basevar basetype -R reference.fasta \
                --regions chr11:5246595-5248428,chr17:41197764-41276135 \
                --batch-count 50 \
                -I 00alzqq6jw.bam \
                -I 09t3r9n2rg.bam \
                -I 0fkpl1p55b.bam \
                -I 13dg1gvsfk.bam \
                -I 17phildszl.bam \
                -I 1dbpgqt0dq.bam \
                -I 1kyws27hoc.bam \
                --output-vcf test.vcf.gz \
                --output-cvg test.cvg.tsv.gz \
                --nCPU 4 && echo "** 5 done **"
        
        Or call variants from bamlist
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        
        .. code:: bash
        
        
            basevar basetype -R reference.fasta \
                --regions chr11:5246595-5248428,chr17:41197764-41276135 \
                --batch-count 50 \
                -L bamfile.list \ 
                --output-vcf test.vcf.gz \
                --output-cvg test.cvg.tsv.gz \
                --nCPU 4 && echo "** 5 done **"
        
        
Platform: UNKNOWN
Classifier: Intended Audience :: Science/Research
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3.7
Classifier: License :: OSI Approved :: BSD License
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Operating System :: POSIX
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS
