Question about Illumina - Nextera Rapid Capture Exome Targeted Regions

[Gebo, Tsumugi A.]

Hello,

 

I am a bioinformatician at UCLA Health and am working on a WES dataset. I understand that the Nextera Rapid Capture Exome bed file from March 7, 2013 (attached for your reference) uses coordinates from the hg19 genome. If I have aligned my data to GRCh38, will I still get accurate results (calling variants) using this Exome target file? Or do you recommend I liftover these targets to GRCh38?

 

Thank you,

Tsumugi

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[Luis Nassar]

Hello, Tsumugi.

Thank you for your interest in the Genome Browser.

As you share, we only offer those array coordinates on hg19 as that is what Illumina makes available on their product site (http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=exomeProbesets).

If your data is aligned to hg38, you will want to have coordinates in that genome. You could lift the hg19 coordinate file, and there are some conversations that suggest it may be safe to do so (https://www.biostars.org/p/362221/), but we cannot offer any guarantees that all coordinates will lift successfully.

If you would like to lift the file, you can see the available options on our liftOver page (http://genome.ucsc.edu/cgi-bin/hgLiftOver).

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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