bow authored Mar 01, 2016 and Peter van 't Hof committed Mar 02, 2016

As mentioned in the documentation[1], the `--custom` flag can
be specified multiple times.

[1] http://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#opt_custom
(cherry picked from commit 5204f4f)

the `failed` flag should be a flag per the documentation
(see:
 http://grch37.ensembl.org/info/docs/tools/vep/script/vep_options.html,
and
http://oct2014.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html )
But, when running, it requires a numeric value.
When running the VEP with verbose mode, it
appears that all boolean flags get converted to 1.
Therefore, I'm setting `failed` to have value 1.