This package can be used to extract the SNPs from VCF from a particular region in the BED file
or the mentioned start and stop position in the BED file. This package also can be used to
extract the gene SNPs from the VCFfile and create a database and store the snp.
The folder consist of a script commonsnpvcf.py which is the main script, additional to that it
has a sample VCF file and a bed file as an example.
- commonsnpvcf.py
- sample_bed_file.bed
- sample_VCF.vcf
- Readme.txt
This is a simple way to go, make sure you keep all the files in a single folder your VCF file as
well as the bed file.
pip install sqlalchemy
python ./commonsnpvcf.py sample_VCF.vcf sample_bed_file.bed Output_table;
The first argument after the commonsnpvcf.py is VCF file from which you want to extract the SNP
either the gene region or the start and stop region.
The second argument after the VCF file is BED file, which has the start and stop region. From
which you can extract the SNP. Please the format of the bed file.
And the third argument is the output file name, what you want to label. This will create a database in sql format
that consist of the SNP from the VCf file for the desire start and stop in BED file.
Please look at the sample VCF file and BED file for file format attached with this package.
All comments and any kind of contribution is useful. The best way is to open an issue or make a pull request.