Removing PCR duplicates in GStacks2

Silvia · August 28, 2025, 1:01pm

hello everyone, i have a question.

when analysing my samples using GStacks2 in galaxy.eu, the output does not provide my with the amount of PCR duplicates removed. When entering the data in GStacks there is no option to select to remove PCR duplicates.

can anyone help?

thanks

Silvia

jennaj · August 29, 2025, 10:17pm

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.