By default, the bgzip function in the Rsamtools package appends ".bgz" to the file name. However, the filterVcf function in the VariantAnnotation package appends ".gz" (see here for Bioc 3.2).

Can you use ".bgz" by default in all functions (or at least in filterVcf)?

ps: this a minor thing, but I thought it can still be useful to fix it for the next release as it can be deconcerting for new users

Thanks for noticing this. The extension has been changed to .bgz in VariantAnnotation 1.17.7.

Valerie