Exome data processing and variant calling based on GRCH38

Question

[nkausthu]

Hi

I am basically working on rare monogenic disorders and now we are in process of shifting the reference to GRCh38 for exome sequencing data analysis. I am not very sure whether I should go for an alt-aware alignment or I can just focus on primary assembly and call the variants. I had come across few discussions regarding this but unfortunately couldn't conclude anything. It would be very helpful if someone can help me to sort this out. Thanks in advance.

Answer 1

[WouterDeCoster]

Heng Li wrote a blog post about this: https://lh3.github.io/2017/11/13/which-human-reference-genome-to-use

[nkausthu]

Yes, I had gone through this article. I am looking if anyone can give specific answer for the following concerns 1) In a clinical context would the alt-aware alignment will make a huge impact on the downstream analysis 2) what is the impact of considering only primary assembly as a reference. Are we going to miss a lot of variants from the exonic regions

Thanks in advance.

[WouterDeCoster]

Alt aware alignment requires alt aware variant calling, which is tough.