<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>

CC BY-SA 4.0
2020-02-27T15:58:14.937Z
2020-02-27T20:35:01.080Z
2020-02-27T20:35:01.080Z
user324810
<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>

CC BY-SA 4.0
2020-02-27T20:33:47.310Z
Yes I also saw that software but I didn't give it a proper test. thanks for your Answer !
user324810
CC BY-SA 4.0
2020-02-27T20:05:25.973Z
2020-02-27T20:05:25.973Z
M__
<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>

<vcf><repeat-elements>
Are there any tools for discovering tandem repeats around a variant in a VCF file?
# 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 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.

**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 !  

---

