Config files

The --config command line option is a handy way configure Octopus. The argument is a text file containing settings for any subset of options (other than config itself). Each line of the file contains a parameter setting in the format

parameter = argument

Comment lines are allowed in the config file are proceeded with #.

It is perfectly fine to specify a config file and explicit command line options, e.g.:

$ octopus --config my-config.config -R reference.fa -I reads.bam -o octopus.vcf

Explicit command line options that are in the config file are ignored.

The configs directory in the main source tree will be used to store useful config files.