# Removing PCR duplicates in GStacks2

**URL:** https://help.galaxyproject.org/t/removing-pcr-duplicates-in-gstacks2/16224
**Category:** Resources
**Tags:** tool-help, stacks2\_gstacks
**Created:** [August 28, 2025, 1:01pm UTC](https://help.galaxyproject.org/t/removing-pcr-duplicates-in-gstacks2/16224 "2025-08-28T13:01:01Z")
**Posts on this page:** 1
**Showing post:** 2

<div class="post-metadata">

### Author: ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [August 29, 2025, 10:17pm UTC](https://help.galaxyproject.org/t/removing-pcr-duplicates-in-gstacks2/16224/2 "2025-08-29T22:17:12Z")

</div>

> [@Silvia](#):
>
> GStacks2

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_

 ![Screenshot 2025-08-29 at 3.13.20 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/6/69c465fc72ef37890dbf6da3728d90e7766118ee.png)

option: Remove read pairs of the same sample that have the same insert length

XRef

- [Stacks](https://catchenlab.life.illinois.edu/stacks/)
- [Stacks: Stacks Manual](https://catchenlab.life.illinois.edu/stacks/manual/)
- [https://groups.google.com/g/stacks-users?pli=1](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. 🙂

---

_[View the full topic](https://help.galaxyproject.org/t/removing-pcr-duplicates-in-gstacks2/16224)._