Interpreting results with one alternative allele

Illumina / ExpansionHunter

A tool for estimating repeat sizes

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Interpreting results with one alternative allele #151

Open gspirito opened 2 years ago

gspirito commented 2 years ago

Hi, if I have results such as this (with only one alternative allele annotated ()):

chr2 202986869 . T . PASS END=202986908;REF=19;RL=40;RU=TA;VARID=AC079354.1;REPID=AC079354.1 GT:SO:REPCN:REPCI:ADSP:ADFL:ADIR:LC 0/1:SPANNING/SPANNING:19/45:19-19/45-46:5/1:58/75:0/0:64.178629

Does this mean that the tool predicts that one allele has 45 TA repeat units (90 base pairs), while the other is equal to the reference (40 base pairs / 20 repeat units)?

Thank you in advance.

egor-dolzhenko commented 2 years ago

I am very sorry for the late reply. Yes, you interpreted the results correctly. You can visualize this call with REViewer: https://github.com/Illumina/REViewer

Did you annotate this repeat yourself or is this a known repeat site?

gspirito commented 2 years ago

Hi, thank you for the reply, this particular locus was one of the ones I annotated.

egor-dolzhenko commented 2 years ago

This sounds good! We are working on a helper tool for automating repeat annotation. If there are other repeats that you'd like to annotate, I would be happy to send you an early development version of this tool.