IUPAC handling in ExpansionHunter

[raphaelbetschart]

Hi,

I'm running into some issues when using EnsembleTR with my ExpansionHunter VCF files.
The main issue is that the reference catalogue includes IUPAC nucleotides (for instance repeat structure AARRG at position chr4:39348424-39348479, taken from https://github.com/Illumina/ExpansionHunter/blob/master/variant_catalog/hg38/variant_catalog.json. This leads to an error in utils.py in the following line:

nucToNumber={"A":0,"C":1,"G":2,"T":3}

Should I just remove this entry or change the reference catalogue manually?
GangSTR and HipSTR catalogue both have the repeat structure AAAAG.

Thanks,
Raphael

[aryarm]

Thanks for reporting this issue, @raphaelbetschart! We've made an attempt at fixing it in gymrek-lab/EnsembleTR#32

Can you try the new code and let us know if you're still having trouble by reopening this issue?