Hi @Silvia
As a guess, is this the tool are you using and the option you are looking for? Maybe you need to adjust the Mode parameter to see this?
Screenshot: Stacks2: gstacks Call variants, genotypes and haplotype
option: Remove read pairs of the same sample that have the same insert length
XRef
- Stacks
- Stacks: Stacks Manual
- https://groups.google.com/g/stacks-users?pli=1 (maybe a useful resources for the protocol since the tools should work about the same everywhere)
Please let us know if this helps! If not, you are welcome to share a screenshot back to help us to understand which tool from the package you are using and your parameters. 