Egor Dolzhenko

Thank you for the question! Although we don't officially support PCR+ data, we know of groups that have shown that ExpansionHunter can detect expansions of many repeats in PCR+ data...

Thanks for the suggestion! We will work on enabling EH to annotate motif changes. Do you have any samples that have such mutations?

@dnil, this sounds good. Once we implement the initial version of motif change annotation algorithm, would you be up for running it on some of your data to confirm that...

Thanks! We will definitely evaluate these repeats. Meanwhile, please consider using larger catalogs distributed with [stranger](https://github.com/moonso/stranger) by @dnil and @moonso. FYI @yjqiu

Sorry for the late reply! Yes, the number of spanning reads is reported in the VCF file. So you could filter the VCF file with a tool like awk or...

Hi Melissa, Thanks for the question! The advanced options correspond to settings with very narrow use cases that are mainly useful for testing the program. The `--aligner` option selects the...

Thanks for the questions! There is no difference in accuracy between seeking and streaming analysis modes. And I will get back to you about the latest runtime/memory benchmarks. But overall,...

Hello William, Sorry about the error. It looks like there is a CRAM parsing bug in the streaming mode. Could you please check if this Linux binary works? (Let me...

Glad to hear it, William! And thanks for checking the memory usage. We will work on reducing memory consumption in the future releases.

Thanks for the question. That's right, "streaming" analysis mode is meant for analysis of larger variant catalogs. It has no other purpose. In the future versions of the program the...