Hi You can use DNAdiff of MuMmer tool. It will detect for you SNPs, Deletions, insertions and other type of structural variation as inversions, trans-locations...etc. DNAdiff compare tow DNA sequences (Your BAC sequence with a reference) but unfortunatly it can not consider the quality of your DNA sequence as other tools do for NGS data. Please have a look to this manual http://nebc.nerc.ac.uk/bioinformatics/documentation/mummer/dnadiff.README. You have to donlowd and install MuMmer and after run DNAdiff with your BAC sequences and the reference it works very well !. Hope that will help

I guess you could use BWA MEM and samtools?

I aligned the BAC contig with bwa mem and used GATK UG to call SNP and Indels . The mapped reads must have a mapping quality above some treshold, mapping quality of 6 was to low. After I increased the minimum seed lenght to 400 for bwa mem my mapping quality was at 60 and GATK UG would call SNPs. To have the GATK UG call Indels on just the aligned BAC contig you need to add some extra parameters:

glm BOTH -minIndelCnt 1 -indelGOP 80 -stand_call_conf 0 -stand_emit_conf 0

The last part of the answer I got from the GATK forum: http://gatkforums.broadinstitute.org/discussion/comment/7086#Comment_7086