How to identify differential microsatellites in GATK ?
Answered
REQUIRED for all errors and issues:
a) GATK version used: gatk4-v4.1.9.0 (Can use also gatk3-v3.8.0)
b) Exact command used: NA
c) Entire program log: NA
Hi,
Which protocol should be used for microsatellite analysis (Somatic mutations)?
1. To identify the microsatellite ?
2. To find significantly differential microsatellite between two populations?
Thank you very much for your contribution to the scientific community,
Arik
-
Thank you for your post, Arye Harel! I want to let you know we have received your question and will be moving it to the Community Discussions -> General Discussion topic, as the Somatic topic is for reporting bugs and issues with GATK.
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.
-
Hi Arye Harel,
Thank you for writing to the GATK forum! We thank you for your patience; I hope we can help you sort this out.
I brought your question to our Mutect2 expert and obtained some pertinent information. Mutect2 is indeed the best tool that we have for identifying microsatellites. That said, the tool will not output information or provide any annotations denoting the specific presence of microsatellites. You can use it to call your indels, but you would need parse out the microsatellites yourself.
In summary, Mutect2 (4.2.6.1) is suitable for helping to identify 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 -
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
-
Hi Anthony,
Thank you very much!
Sorry for the late response.
I am looking in to it now. A. -
Hi,
I see you sent an improved answer on my duplicated post at: https://gatk.broadinstitute.org/hc/en-us/community/posts/6809415185947-Is-Somatic-short-variant-discovery-the-correct-Pipeline-to-identify-differential-microsatellites-
Sorry for the confusion.
Maybe it is better to close current post to prevent further confusion.
Thank you.
Arik.
Please sign in to leave a comment.
5 comments