<ol>
<li><code>HFE|LOC108783645</code> is <a href="https://www.ncbi.nlm.nih.gov/gene/108783645" rel="nofollow noreferrer">https://www.ncbi.nlm.nih.gov/gene/108783645</a>. You can use biomaRt to go from the <code>LOCxxxx</code> ID to location. Searching by <code>HFE</code> will give you a different location though, so you might have to account for such eventualities. It is a long and often manually intensive process.</li>
<li>You should be able to use entrez-direct/eutils to go from rsID to position</li>
<li>Unless there's some sort of natural language processing API, <code>codon 109 of exon 3 of beta globin gene</code> cannot be parsed by existing APIs (Unless it's always <code>codon X of exon Y of Z</code>, in which case you could use <code>grep</code> too get the components. Even so, going from exon + codon + codon base change to exact base location will require a lot of wrangling.</li>
</ol>

CC BY-SA 4.0
2020-05-18T23:58:47.787Z
2020-05-18T23:58:47.787Z
Ram RS
<p>I am looking for a given mutation in <a href="https://us.v-cdn.net/5019796/uploads/FileUpload/c4/d9900bc2df5ef6ed48c9709bb16de9.png" rel="nofollow noreferrer">IGV</a>, which accepts coordinates in the form of</p>

<pre><code>chr&lt;X&gt;:&lt;Y&gt;
</code></pre>

<p>Where X is the chromosome number and Y is the base location in that chromosome.</p>

<p>Eg. <code>chr6:26091179</code> which has the following attributes:</p>

<pre><code>Gene: HFE|LOC108783645
Marker: rs1799945
Position: chr6:26091179
</code></pre>

<p>Additionally, an interval can be written like</p>

<pre><code>chr&lt;X&gt;:&lt;Y&gt;-&lt;Z&gt;
</code></pre>

<p>So basically from base located at Y to Z.</p>

<p><strong>My questions are:</strong></p>

<p><strong>1)</strong> How do I convert <code>HFE|LOC108783645</code> to <code>chr6:26091179</code> (and vice-versa)?</p>

<p><strong>2)</strong> How do I convert <code>rs1799945</code> to <code>chr6:26091179</code> (and vice-versa)?</p>

<p><strong>3)</strong> On a different example, how do I convert something like <code>codon 109 of exon 3 of beta globin gene (GTG-&gt;TTG)</code> to <code>chr&lt;X&gt;:&lt;Y&gt;</code> (or <code>chr&lt;X&gt;:&lt;Y&gt;-&lt;Z&gt;</code>)?</p>

<p>Why are there so many ways to specify positions in genes? For me the most clear way is <code>chr&lt;X&gt;:&lt;Y&gt;</code>, all the others leave me guessing...</p>

CC BY-SA 4.0
2020-05-18T23:53:54.103Z
You should look at HGVS conventions used to refer to positions with respect to reference sequences. Remember, not even `chr:pos` notations are independent of reference sequence versions. `chr6:26091179` in GRCh38 is not the same in GRCh37.
Ram RS
<gene><genome><phylogenetics><igv>
How can I convert codon coordinates to genomic position?
# How can I convert codon coordinates to genomic position?

(Asked by: username_0 on 2020-05-18)

I am looking for a given mutation in IGV, which accepts coordinates in the form of
chr:

Where X is the chromosome number and Y is the base location in that chromosome.
Eg. chr6:26091179 which has the following attributes:
Gene: HFE|LOC108783645
Marker: rs1799945
Position: chr6:26091179

Additionally, an interval can be written like
chr:-

So basically from base located at Y to Z.
My questions are:
1) How do I convert HFE|LOC108783645 to chr6:26091179 (and vice-versa)?
2) How do I convert rs1799945 to chr6:26091179 (and vice-versa)?
3) On a different example, how do I convert something like codon 109 of exon 3 of beta globin gene (GTG->TTG) to chr: (or chr:-)?
Why are there so many ways to specify positions in genes? For me the most clear way is chr:, all the others leave me guessing...

**Tags:** gene, genome, phylogenetics, igv
> **Comments:**
> **username_1**: You should look at HGVS conventions used to refer to positions with respect to reference sequences. Remember, not even `chr:pos` notations are independent of reference sequence versions. `chr6:26091179` in GRCh38 is not the same in GRCh37.  

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## 1 answers

### Answer by username_1 on 2020-05-18. Score: 1 | Accepted answer

1. `HFE|LOC108783645` is <https://www.ncbi.nlm.nih.gov/gene/108783645>. You can use biomaRt to go from the `LOCxxxx` ID to location. Searching by `HFE` will give you a different location though, so you might have to account for such eventualities. It is a long and often manually intensive process.
2. You should be able to use entrez-direct/eutils to go from rsID to position
3. Unless there's some sort of natural language processing API, `codon 109 of exon 3 of beta globin gene` cannot be parsed by existing APIs (Unless it's always `codon X of exon Y of Z`, in which case you could use `grep` too get the components. Even so, going from exon + codon + codon base change to exact base location will require a lot of wrangling.


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