text: user4413: I know for example PolyX from Pierre's Jvarkit to find the number of repeated REF bases (homopolymers) around a position in a VCF file as described here 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.
  
  user4413: After researching a bit, I found a couple of tools that take as input BAM files. I did not test them yet:
  
  GangSTR
  lobSTR
  hipSTR
  Tandem Repeat Finder (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.
  
  user3848: The old program for doing this last updated in 2016 is Tandem Repeat Finder (TRF) here. 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.
  
original_text: 4413: <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>
   4413: <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>
   3848: <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>
  