Can GATK pipelines be used for Ion torrent data?
Hello Team GATK,
Can the GATK pipeline be used for Ion torrent data (GATK4.2 best practices)? Or is there any specific pipeline that can be used for single-end read for the Ion torrent?
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Thank you for your post, DHWANI DHOLAKIA! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions.
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Hi DHWANI DHOLAKIA,
Thank you for writing into the forum with your question and your patience while we got back to you.
Yes, you can run GATK on Ion torrent data. Unfortunately, we are not experts on Ion torrent data so I am not familiar with specifically what you need to do. You can reach out to other Ion torrent users to see what they have done in the past. GATK was built and tested with Illumina data so that is where it performs the best.
I do know that you may need to make some adjustments and to make sure your read groups are set up properly with GATK. Here is an article about read groups: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups. For the platform (PL), you can use ION_TORRENT. In addition, in the MarkDuplicates step, you should disable optical duplicates because those are specific to Illumina data.
- Here is a helpful biostars post: https://www.biostars.org/p/377297/
- And a helpful post from our legacy forum: https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2013-06-06-2013-02-12/2568-how-to-define-Read-group-for-iontorrent-data
Please let me know if you have any other questions and I'll try my best to answer them!
Best regards,
Genevieve
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