<p>The keyword to look for is 'liftover'. Here's liftover information for translating from GRCh38 to CHM13:</p>
<p><a href="https://github.com/pangenome/chm13-grch38-liftover" rel="nofollow noreferrer">https://github.com/pangenome/chm13-grch38-liftover</a></p>
<p>If this isn't what you need, I suggest asking the pangenome people directly via a github issue:</p>
<p><a href="https://github.com/pangenome/chm13-grch38-liftover/issues" rel="nofollow noreferrer">https://github.com/pangenome/chm13-grch38-liftover/issues</a></p>

CC BY-SA 4.0
2024-11-30T10:58:05.470Z
2024-11-30T10:58:05.470Z
gringer
<p>I want to a mapping that has linear coordinates and corresponding pangenome (e.g., .gfa format) locations. For example, this type of information could say that region chr 1 1000-2000 corresponds to nodes 104-108.</p>
<p>I have tried vg find, vg indexing tools, and manual .gfa analysis, but I could not get this information.</p>
<p>Any of these would be a solution:</p>
<ul>
<li>A description of an algorithm to extract this information from a .gfa file</li>
<li>A file where this mapping is explicitly given</li>
<li>A tool that works to retrieve this information</li>
</ul>

<genome><reference-genome><sequence><graphs><pangenome>
How do I figure out pangenome location of hg38 coordinates?
# How do I figure out pangenome location of hg38 coordinates?

(Asked by: username_0 on 2024-11-29)

I want to a mapping that has linear coordinates and corresponding pangenome (e.g., .gfa format) locations. For example, this type of information could say that region chr 1 1000-2000 corresponds to nodes 104-108.

I have tried vg find, vg indexing tools, and manual .gfa analysis, but I could not get this information.

Any of these would be a solution:

* A description of an algorithm to extract this information from a .gfa file
* A file where this mapping is explicitly given
* A tool that works to retrieve this information

**Tags:** genome, reference-genome, sequence, graphs, pangenome

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## 1 answers

### Answer by username_1 on 2024-11-30. Score: -1

The keyword to look for is 'liftover'. Here's liftover information for translating from GRCh38 to CHM13:

<https://github.com/pangenome/chm13-grch38-liftover>

If this isn't what you need, I suggest asking the pangenome people directly via a github issue:

<https://github.com/pangenome/chm13-grch38-liftover/issues>


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