Conf file

Annotate with an OakVar configuration file

For repeated jobs, using a .yml file with job definition is handy.

For example, consider the following ov run job:

ov run input.vcf -a clinvar cosmic dbsnp -t csv

The configuration of this job can be written in conf.yml file as follows:

run:
    annotators: 
    - clinvar
    - cosmic
    - dbsnp
    report_types: csv

Then, this file can be used as follows.

ov run input.vcf -c conf.yml

which will work in the same way as the first ov run command.

Below are the correspondence between ov run options and the fields in package .yml files.

ov run option	type	package file (.yml) option
-a	list	annotators
-p	list	postaggregators
-t	list	report_types
-n	string	run_name
-d	string	output_dir
--clean	bool	clean
--genome	string	genome
-i	string	input_format
--startat	string	startat
--endat	string	endat
--skip	list	skip
--keep-temp	bool	keep_temp
--mp	integer	mp
--primary-transcript	string	primary_transcript
--module-options	dict	module_options
--vcf2vcf	bool	vcf2vcf
--logtofile	bool	logtofile
--ignore-sample	bool	ignore_sample