<p>What's your reference for the definition of STRs? I think it is still ambiguous among the community. Wikipedia states motifs of >=2 bp. However other references include homopolymers as well:<br>
<a href="http://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4267.html" rel="nofollow noreferrer">Source 1</a>, <a href="http://www.cell.com/ajhg/fulltext/S0002-9297(17)30382-8" rel="nofollow noreferrer">source 2</a> and <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054066/" rel="nofollow noreferrer">source 3</a>.</p>

CC BY-SA 3.0
2017-11-08T22:41:11.450Z
2017-11-09T08:12:52.643Z
2017-11-09T08:12:52.643Z
Giuseppe Narzisi
<p>I'm reading <a href="https://www.biorxiv.org/content/early/2017/10/24/196311" rel="nofollow noreferrer">a preprint on a new somatic variant discovery tool</a>, and the first sentence of the Discussion section has me confused.</p>

<blockquote>
  <p><em>Across the four datasets analyzed in this study, we discovered that the major source of disagreement between callers originates from somatic variants called within STRs, in particular if the motif is two base pairs or longer.</em></p>
</blockquote>

<p>The "<em>two base pairs or longer</em>" bit is what confuses me. I interpreted "motif" as referring to the short tandem repeats (STRs), which are by definition 2 bp or longer. A motif of &lt; 2 bp is...a homopolymer, not really a motif in the common sense.</p>

<p>Am I missing something here? Or is this simply an awkward word choice on the part of the authors?</p>

CC BY-SA 3.0
2017-11-08T21:15:28.740Z
I doubt you’re missing anything, I suspect they’re using confused wording.
Devon Ryan
<variant-calling><genomics><repeat-elements>
What does "motif 2 bp or longer" mean?
# What does "motif 2 bp or longer" mean?

(Asked by: username_0 on 2017-11-08)

I'm reading [a preprint on a new somatic variant discovery tool](https://www.biorxiv.org/content/early/2017/10/24/196311), and the first sentence of the Discussion section has me confused.

> *Across the four datasets analyzed in this study, we discovered that the major source of disagreement between callers originates from somatic variants called within STRs, in particular if the motif is two base pairs or longer.*

The "*two base pairs or longer*" bit is what confuses me. I interpreted "motif" as referring to the short tandem repeats (STRs), which are by definition 2 bp or longer. A motif of < 2 bp is...a homopolymer, not really a motif in the common sense.

Am I missing something here? Or is this simply an awkward word choice on the part of the authors?

**Tags:** variant-calling, genomics, repeat-elements
> **Comments:**
> **username_1**: I doubt you’re missing anything, I suspect they’re using confused wording.  

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## 1 answers

### Answer by username_2 on 2017-11-08. Score: 4 | Accepted answer

What's your reference for the definition of STRs? I think it is still ambiguous among the community. Wikipedia states motifs of >=2 bp. However other references include homopolymers as well:  
[Source 1](http://www.nature.com/nmeth/journal/v14/n6/full/nmeth.4267.html), [source 2](http://www.cell.com/ajhg/fulltext/S0002-9297(17)30382-8) and [source 3](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5054066/).


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