Egor Dolzhenko

Hi Aarthi, Thank you for the question. EHv4 uses a different STR genotyping algorithm than EHv3. These two versions can output discordant genotypes in cases when there are many poorly/ambiguously...

Hi Katerina, Thanks for the question. Would you be able to share your catalog of CODIS loci? We could run them through our benchmarking pipeline to assess the error rate....

Hello Sergey, Unfortunately there are no publicly available documents describing the pipeline yet. But there is a good chance that we will put together a detailed description of the pipeline...

Thank you for catching this! The error was caused by a missing genotype, which prevents REViewer from determining haplotype sequences. I just updated to program to generate the following error...

Thanks for the suggestion! Generating an empty plot (perhaps with a warning message) sounds good. I'll implement this.

Thanks for the question! Detecting longer motifs tends to be more error-prone. This is because a read can span relatively few motifs longer than 20bp and hence a small number...

Thanks for the question Karynne. The algorithm for detecting in-repeat reads has changed between versions 0.6.2 and 0.9.0. So, it would be best to limit the analysis to STR profiles...

Thank you for the questions. In many cases identifying and counting motifs in reads is straightforward. But sometimes it gets more complicated because of mosaicim, sequence composition changes, nested repeats,...

Thank you for the question. Yes, Truvari is a sequence-level benchmark. In my opinion, evaluating the accuracy of motifs and their counts is a much more elusive task. For example,...

Thanks for reporting this, Joel! Is it at all possible that TRGT is being run on a BAM file with subreads (instead of a BAM file with consensus HiFi reads)?...