Question

Translating thinks like (c.2450-118A>G) to a position in IGV

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2.5 years ago

McKenna • 0

I often see things encoded with this notation (c.2450-118A>G) how does one convert that to something usable in IGV?

Thanks!

igv • 975 views

ADD COMMENT • link 2.5 years ago by McKenna • 0

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IGV can handle variants in these formats. So your could convert your HGVS format data into a compatible format (perhaps VCF). Ensembl variant recoder may do the trick.

ADD REPLY • link 2.5 years ago by GenoMax 141k

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Ahh, that’s it! thanks!

ADD REPLY • link 2.5 years ago by McKenna • 0

score 1 · Answer 1 · 2021-10-24

This looks a bit like HGVS notation, though it's not clear what transcript this is associated with (I believe the c. indicates that it is associated with a coding sequence of some transcript, but since we don't know that from your post, we can't provide an answer of where it actually is)

Some links

https://variantvalidator.org/service/validate/ http://varnomen.hgvs.org/bg-material/simple/ for example