Egor Dolzhenko

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 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...

Hello Anne-Sophie, At the moment ExpansionHunter outputs logging information to the standard error. We could definitely add support for printing logs to a file. Is the way logging done currently...

Thank you for the request! We are currently working on assessing our ability to call these types of expansions. Do you by any chance have samples that contain FAME expansions?...

@fjmuzengyiheng: Thanks for the question! Could you please visualize alignments of reads to this repeat with [REViewer](https://github.com/Illumina/REViewer)? This will tell us if this repeat definition is appropriate for your sample....

We will likely need to make some code changes to add proper support for this repeat. @fjmuzengyiheng, would you be interested to contribute to this effort? The WGS data with...

Hi Konstantin, Katerina, Sergey, I am sorry this fell through the cracks. The latest changes to the build script are aimed at decoupling external dependencies from ExpansionHunter itself: - The...

That's exactly right, Andreas! Emi: EH extracts mates of reads aligned close to the repeat, even if those mates are located on other chromosomes. Here is a quick cartoon illustrating...

Glad we could help! Please don't hesitate to reach out if you run into any other issues!

Thanks for the question! There is no explicit cutoff on the number of spanning reads at the moment. We will work on adding something like a genotype quality score to...