Streamline the use of `.vcf.gz` versus `.bcf`

[famosab]

• At the moment different tools need different inputs. It would be good to do one check of the pipeline and decide where .vcf.gz files are really needed and replace every other occurence with .bcf files.

• The merge_callsets rule only allows either .vcf.gz or .bcf as raw input files. This needs to be reflected in the docs of NCBench or the workflow needs to be adapted to transform raw .vcf files into either bgzipped .vcf.gz or .bcf files.