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Make sure toucan creates bed track for varda based on all calls (including ref calls!), but only upload variants in vcf.
If we wouldn't do this, varda would show much higher frequencies than we actually want to show:
Varda calculates frequencies based on how many samples are covered at that position.

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.