merge aligned read pairs that overlap - keep the bases that match the reference

Question

[Richard]

Hi all,

I have aligned paired-end genome data that was sequenced with 150bp reads. The average insert size is just 200bp so there are lots of read pairs with significant overlap of their alignments.

I see that there are lots of tools for merging fastq data and at least one that clips overlapping read alignments.

I'm looking for a tool that uses a conservative approach that when merging or clipping overlapped read alignments, chooses the bases that match the reference over bases with high sequencing quality.

thanks, RIchard