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Exome data processing and variant calling based on GRCH38

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.

grch38 alt-aware alignment variant calling
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updated by WouterDeCoster WouterDeCoster • written by nkausthu • nkausthu

1 answer

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

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written by WouterDeCoster WouterDeCoster

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.

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written by nkausthu • nkausthu

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

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written by WouterDeCoster WouterDeCoster

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