I want to find specific SNPs in my evolved, haploid strain. Is it enough if I just map it to the reference genome etc…Or I should merge the BAM format of it with the BAM format of the parental strain into one BAM? Then go forward with the procedure?
If you have parental strain data you should most definitely include it in your analysis! Typically, you do not have to merge the BAM datasets for this, but it is enough to do joint variant calling with all your BAM datasets. Freebayes, for example, has the option to Run in batch mode and Merge Output VCFs, which is how you could make the tool consider both of your BAMs simultaneously during variant calling.
If all of the 6 evolved strains share the same parent, then go with a. and analyze everything together. This will alow you to discard SNPs brought into all evolved strains via that common ancestor efficiently later on.
If some of your strains have evolved from distinct parents, i.e., represent a completely different experiment, go with b. and analyze those samples separately.