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Illumina / ExpansionHunter

A tool for estimating repeat sizes
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Is it possible to convert EHdn single sample STR profiles to EH variant catalog format? #135

Open hevmarriott opened 3 years ago

hevmarriott commented 3 years ago

Hi there,

I want to genotype novel/non-reference repeats identified with Expansion Hunter Denovo for single samples - is there a helper script to convert the STR profiles generated to a variant catalog format?

Best,

Heather

egor-dolzhenko commented 3 years ago

Hi Heather,

This is a great question. Please take a look at an earlier discussion here.

One of my teammates is working on such a script, however we are not sure when it would be ready for release yet.

If by any chance you have relevant truth data or you are interested in participating in the development of this script, please feel free to reach out.

Best wishes, Egor

hevmarriott commented 3 years ago

Hi Egor,

Thanks for this - the script is 100% what I am after! Would this script be available to incorporate into a pipeline intended for public use?

Best,

Heather

egor-dolzhenko commented 3 years ago

Hi Heather,

We will definitely release this script as soon as we have the first working version. Meanwhile perhaps you could consider using the script referenced in this issue?

Best wishes, Egor