1
$\begingroup$

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

chr<X>:<Y>

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<X>:<Y>-<Z>

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<X>:<Y> (or chr<X>:<Y>-<Z>)?

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

$\endgroup$
1
  • $\begingroup$ 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. $\endgroup$
    – Ram RS
    May 18 '20 at 23:53
1
$\begingroup$
  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.
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.