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We would like to know how does GATK handle the situation where an insert in a library is sequenced from both ends (read 1 and read 2), and the insert is sufficiently short that the reads overlap. This gives rise to a situation where the same stretch of DNA from the same insert is read twice, so it is effectively a duplicated (sub)read. Ideally the overlap should only be counted once for the purposes of polymorphism discovery. We understand that GATK now has functionality to handle this situation by merging the fragments when they overlap before doing SNP calling; is this the case?