Closed npatel22526 closed 4 years ago
Hi @npatel22526,
Apologies for the slow reply regarding your question. Yes, we have tested HipSTR using WES data, and in my opinion it still works quite well. However, there are a few intricacies that make WES calls more challenging than WGS calls:
HipSTR is designed to deal with issue 2, as it learns a stutter model for each STR locus. Ideally, if you're analyze WES data, you should jointly genotype a reasonably sized cohort (>20 individuals) so that HipSTR can learn an appropriate stutter model for each locus. Y
The WES intricacies will also affect several aspects of the HipSTR genotypes, most notably:
You'll need to fine-tune your post-genotyping filtering criteria to address these issues.
Hope that helps but let me know if you have any additional questions!
Hello,
Thanks for your detailed response and sorry I completely missed it. I am mostly interested in Mono and Di nucleotide repeats and almost all of them are on < 30 bp in length so hoping to get the best out of our reads with the length of 150bps. Appreciates, your suggestion on filtering.
Best, Nick
Hello,
In our experience HipSTR works great with WGS but is it ever tested/tried/experimented with WES or Panel sequencing data ? If so curious to know how well it performs ?
Best, Nick