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What is a genomic range that would almost always get decent WGS coverage but is never covered by WES?

So some intergenic range that isn't hard to sequence and is nowhere near the periphery of a gene that would be on an exome kit.

wes wgs
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updated by i.sudbery i.sudbery • written by Jeremy Leipzig Jeremy Leipzig

What would you want to do with such a region(s)?

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written by GenoMax GenoMax

use it to know if I was looking at wgs or wes

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written by Jeremy Leipzig Jeremy Leipzig

You could take BED regions from some of the common WES kits and then create a "superset" region file to subtract from the genome (and perhaps remove blacklisted regions as well).

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written by GenoMax GenoMax

2 answers

What about some of the well known enhancer regions, the globin locus LCR? Likely to be highly sequenceable, and yet not on exome panels.

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written by i.sudbery i.sudbery

I don't really understand this question?

Any intron is going to get good relative coverage in WGS over WES... Anything over 5 kb (probably even 1 kb) away from a targeted exon will have 0 reads (in WES) - outside of background reads... so like avoid regions with transposon/repeat elements. If you want to go over the top best is probably an intron with high conservation.

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written by benformatics benformatics

i think you did understand the question, i just wanted a chr:start-end region to use as a litmus test.

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written by Jeremy Leipzig Jeremy Leipzig

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