For a PE-reads BAM file, I would like to keep only those pairs that map to a unique location. I know I can filter reads with multiple mappings with samtools (
-bq 1), but this doesn't take into account paired information. I mean, if mate #1 maps uniquely to locus A, and mate #2 maps both to A and B, then we should be confident that #2 maps to A. Using samtools
-bq 1 removes mate #2 in this case but I would like to keep it (because of the uniqueness of mate #1). Any idea how to solve this?