Answers.Body: <p>After researching a bit, I found a couple of tools that take as input BAM files. I did not test them yet:</p>
  
  <ul>
  <li><a href="https://github.com/gymreklab/GangSTR" rel="nofollow noreferrer">GangSTR</a></li>
  <li><a href="https://github.com/mgymrek/lobstr-code" rel="nofollow noreferrer">lobSTR</a></li>
  <li><a href="https://github.com/tfwillems/HipSTR" rel="nofollow noreferrer">hipSTR</a></li>
  <li><a href="https://tandem.bu.edu/trf/trf.html" rel="nofollow noreferrer">Tandem Repeat Finder</a> (thanks to Michael G.'s answer)</li>
  </ul>
  
  <p>If I find more tools, I will update this post. After testing them, I will come back to share my feedback.</p>
  
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Answers.Body: <p>The old program for doing this last updated in 2016 is Tandem Repeat Finder (TRF) <a href="https://tandem.bu.edu/trf/trf.html" rel="nofollow noreferrer">here</a>. This will not find a microsatellite sequence at a given variant, but instead find all tandem repeats in the genome and their position. It has been around for a long time.</p>
  
  <p>You would then simply screen this output against the position of your variant. TRF may have been modified however to perform a search within given nucleotide boundaries.</p>
  
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Answers.Text: Yes I also saw that software but I didn't give it a proper test. thanks for your Answer !
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Body: <p>I know for example <code>PolyX</code> from Pierre's <a href="http://lindenb.github.io/jvarkit/" rel="nofollow noreferrer"><code>Jvarkit</code></a> to find the number of repeated REF bases (homopolymers) around a position in a VCF file as described <a href="https://www.biostars.org/p/140069/" rel="nofollow noreferrer">here</a> exists.</p>
  
  <p>I would like to know however if there tools that describes tandem repeats around a reported variant (TR) up to 6 repeated bases. I can imagine 3 different scenarios:</p>
  
  <p><strong>Scenario 1:</strong></p>
  
  <pre><code>chrK    posY    C     G
  
  TR of (ATC)
  ____________v
  ATCATCATCATCGATGATAC
  </code></pre>
  
  <p><strong>Scenario 2:</strong></p>
  
  <pre><code>chrK    posY    A     T
  
               TR of (AACT)
              v____________
  CAGTCGATTGGATAACTAACTAACT
  </code></pre>
  
  <p><strong>Scenario 3:</strong></p>
  
  <pre><code>chrK    posY    C     A
  
  TR of (AG)    TR of (AG)
  ____________v__________
  AGAGAGAGAGAGCAGAGAGAGAG
  </code></pre>
  
  <p>If you know any tools in mind that can be used for VCFs, I'd really appreciate citing them.</p>
  
  <p>Thanks in advance.</p>
  
Tags: <vcf><repeat-elements>
Title: Are there any tools for discovering tandem repeats around a variant in a VCF file?
ThreadText: # Are there any tools for discovering tandem repeats around a variant in a VCF file?
  
  (Asked by: username_0 on 2020-02-27)
  
  I know for example `PolyX` from Pierre's [`Jvarkit`](http://lindenb.github.io/jvarkit/) to find the number of repeated REF bases (homopolymers) around a position in a VCF file as described [here](https://www.biostars.org/p/140069/) exists.
  
  I would like to know however if there tools that describes tandem repeats around a reported variant (TR) up to 6 repeated bases. I can imagine 3 different scenarios:
  
  **Scenario 1:**
  
  ```
  chrK    posY    C     G
  
  TR of (ATC)
  ____________v
  ATCATCATCATCGATGATAC
  
  ```
  
  **Scenario 2:**
  
  ```
  chrK    posY    A     T
  
               TR of (AACT)
              v____________
  CAGTCGATTGGATAACTAACTAACT
  
  ```
  
  **Scenario 3:**
  
  ```
  chrK    posY    C     A
  
  TR of (AG)    TR of (AG)
  ____________v__________
  AGAGAGAGAGAGCAGAGAGAGAG
  
  ```
  
  If you know any tools in mind that can be used for VCFs, I'd really appreciate citing them.
  
  Thanks in advance.
  
  **Tags:** vcf, repeat-elements
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2020-02-27. Score: 1 | Accepted answer
  
  After researching a bit, I found a couple of tools that take as input BAM files. I did not test them yet:
  
  * [GangSTR](https://github.com/gymreklab/GangSTR)
  * [lobSTR](https://github.com/mgymrek/lobstr-code)
  * [hipSTR](https://github.com/tfwillems/HipSTR)
  * [Tandem Repeat Finder](https://tandem.bu.edu/trf/trf.html) (thanks to Michael G.'s answer)
  
  If I find more tools, I will update this post. After testing them, I will come back to share my feedback.
  
  
  ---
  
  ### Answer by username_1 on 2020-02-27. Score: 1
  
  The old program for doing this last updated in 2016 is Tandem Repeat Finder (TRF) [here](https://tandem.bu.edu/trf/trf.html). This will not find a microsatellite sequence at a given variant, but instead find all tandem repeats in the genome and their position. It has been around for a long time.
  
  You would then simply screen this output against the position of your variant. TRF may have been modified however to perform a search within given nucleotide boundaries.
  
  > **Comments:**
  > **username_0**: Yes I also saw that software but I didn't give it a proper test. thanks for your Answer !  
  
  ---
  
  