Is there a split read SV caller that I can use to call Structural Variants (SV) on aligned BAC contigs?
The BACs contigs are ca 150 kb and are aligned in either one primary alignment or in multiple primary (split) alignments by bwa-mem. Some of the smaller SV's are within the primary alignments (up to 5000 bp), others are from one primary alignment to another primary alignment.
Are there any tools for calling the SV's based on the split BAC alignment? Or could I just use an NGS split alignment tool like Pindel?