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
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