Can I Use SureSelect v7 on Exome Data Captured with SureSelect v6?

Question

[George]

I'm currently working on a variant calling pipeline for some Whole Exome Sequencing (WES) data, and I've encountered a bit of a dilemma. The exome capture kit that was originally used for my data is the Agilent SureSelect DNA - SureSelect Human All Exon V6 r2, which is based on the hg19 (GRCh37) reference genome. However, I want to use SureSelect v7, which is designed for the hg38 reference genome.

My question is: Can I safely use the SureSelect v7 bed or would it be too risky given that the original data was captured with a kit based on hg19? What are the potential pitfalls of this approach, and would it significantly affect the accuracy or reliability of the variant calls? Any insights or suggestions would be greatly appreciated!

Answer 1

[Tm]

Exome kits are never constructed with a specific version of the reference genome in mind; instead, they are developed by creating probes that can capture a selection of genes of interest.

You must not utilise a bed file from one capture kit for another since they capture different regions of the genome. And, to my knowledge, Agilent SureSelect DNA - SureSelect Human All Exon V6 is one of the best kits with comprehensive exome coverage.

So, download the hg38 bed file for Agilent SureSelect DNA - SureSelect Human All Exon V6 r2 from the Agilent Sure Design website (https://earray.chem.agilent.com/suredesign/) and use it for analysis.

[George]

Hey, thank you for your comprehensive response, didn't know all that.