Can anyone suggest how to use samtools to filter only hits where there is a insertion in the reference that splits the sequence hit roughly by the middle?
My sequences are in the range of 100-1000bp and were aligned using "bwa bwasw -z 100".
I don't expect perfect hits, so mismatches and small indels can occur at both ends of the hit, but I am looking for insertions in the reference in the middle that are 10x+ bigger than any small indels at both ends.
I don't have paired ends.