When getting SnpEff from the upstream source repository, the configuration file
snpEff.config usually sits next to the jar; this is not the case for the Debian
packaging, because the jar is in /usr/share/java.  So I am shipping a default
/etc/snpeff/snpEff.config file and it will be copied into
~/.snpEff/snpEff.config, which will be used, if the latter does not exist and
if no other config file is given in the command line invocation.

Moreover, by default data downloaded from the Internet by snpEff will be put
into ~/.snpEff/data. The users can change this by editing their per-user config
file ~/.snpEff/snpEff.config or by providing another config file on the command
line.

 -- Pierre Gruet <pgt@debian.org> Tue, 08 Feb 2022 23:44:18 +0100