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

Question

[Jeremy Leipzig]

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.

[GenoMax]

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

[Jeremy Leipzig]

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

[GenoMax]

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).

Answer 1

[i.sudbery]

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

Answer 2

[benformatics]

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.

[Jeremy Leipzig]

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