Indels removed #20
Description
Somehow, somewhere along the line, it looks like indels were being removed from the vcf file by the bcftools_view_multiallelicsites rule.
It looks to be the flag at line 7 (--exclude-types indels).
Honestly, I don't know why or how that ended up there, but it was a bit of a major derp to just remove all indels from the vcf file given we're looking at SNP's/indels.
I tested removing that flag altogether, which seemed to work just fine and the downstream vcf file loaded into scout just fine from what I can see.
So get rid of this --exclude-types indels flag that probably shouldn't be there anyway