Questions regarding the detection of variants (SNPs and Indels) in mammal
This is close to what many people do. May I add:


between 4 and 5 you might want to add read groups using Picard. This will allow GATK to work. For this purpose (in case picard gives you issues), some time ago I made this. 
filtering with BCFtools is somewhat uncomfortable (for me at least). I would suggest you to plot the distribution of every variable in the INFO and GENOTYPE fields of the VCF file and understand their distribution and meaning. It could vary a lot and there is no one-size-fits-all threshold.
For that purpose, some time ago I made this and this.