I have BAC contig, assembled from sanger sequences, that I want to use for quality control on my short read based SNP and indel call's.
Which tool can I use to align the BAC sequence against the reference, and which tool do I then use to call SNP and Indel?
Or is it smarter just to use the Sanger sequences directly? To align them with BWA-mem and have GATK (UG or HC) call SNP and Indel?