converts VCF into GA4GH
To begin: Turn on a virtual environment and pip install requirements
Have mongodb running(if you want db output).
python scr.py -i vcfFileName.vcf.gz
optional commands: "-db DatabaseName" "-ch chromosomeName" "-pb AnyTextHereWorks"
When running the program, input file (-i filename) is required, specifying database (-db databasenameyouwant) is optional. If you do not specify -db, only directory structured output will be created. You can also specify chromosome with -ch chromosomeName, this is optional and if you do not specify, the entire file will be fetched. If you wish to have .pb as output instead of .txt into the directory use the extension -pb pb. If this is specified it will output only to .pb. If this is not specified it will output to .txt. This command is optional and can be used with or without outputting to database.