Is "Somatic short variant discovery" the correct Pipeline to identify differential microsatellites?

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Arye Harel

• June 23, 2022 11:41

Regarding the "Somatic short variant discovery" pipeline (https://gatk.broadinstitute.org/hc/en-us/articles/360035894731).

Since this pipeline  allows identifying INDELS, is it the correct protocol to identify significantly differential microsatellites?

 

Thank you ,

 

Arik

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  Anthony DiCi

  • June 23, 2022 15:48

  Thank you for your post, Arye Harel ! 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. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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  Anthony DiCi

  • September 22, 2022 14:50

  Hi Arye Harel,

  *I see you wrote nearly duplicate posts. I've just responded to your other inquiry with the below response. I've made some slight alterations for clarity.*

  I brought your question to our Mutect2 expert and obtained some pertinent information. Mutect2 is indeed the best tool that we have for identifying significantly differential microsatellites. That said, the tool will not output information or provide any annotations denoting the specific presence of significantly differential microsatellites. You can use it to call your indels, but you would need parse out the significantly differential microsatellites yourself.

  In summary, Mutect2 (4.2.6.1) is suitable for helping to identify significantly differential microsatellites, but it involves some additional work to pin them down.

  I hope this helps clarify your question! Thank you again for your patience and valued contribution to the GATK forum. Please do not hesitate to reach out if you have any other questions.

  Best,
  Anthony

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  Anthony DiCi

  • September 29, 2022 15:03

  Hi Arye Harel,

  We haven’t heard from you in a while so we will be closing out your ticket in our system. If you still require assistance, you need only respond to this thread, and we’ll create a follow-up ticket to pick up where we left off.

  Thank you again for contributing to our GATK forum!

  Best,

  Anthony

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  Arye Harel

  • October 03, 2022 14:09

  Hi Anthony,
  Thank you very much!
  Sorry for the late response.
  I am looking in to it now. A.

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  Anthony DiCi

  • October 06, 2022 15:55

  Hi Arye Harel,

  You commented on your duplicate post that the feedback on this post may have helped you solve your inquiry. Do you have any further questions before I go ahead and close this ticket out as well?

  Thank you again for being a valued members of the GATK community!

  Best,

  Anthony

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  Anthony DiCi

  • October 13, 2022 17:05

  Hi Arye Harel,

  We haven't heard from you in a while so we're going to close out this ticket. If you still require assistance, simply respond to this email and we'll be happy to pick up where we left off!

  Kind regards,

  Anthony​

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