Hi all!

I am struggling for weeks with this problem and I hope someone can help. I would like to compare the target regions of human exome sequencing from two different enterprises with what would be the “whole reference exome” for humans. To do that, I used the following logic:

1. Downloaded hg38 GTF on gencode (release 41)
2. Isolated entries of protein-coding and exon only
3. Isolated entries only in the 24 chromosomes
4. Merged different transcripts sharing exons, using Bedtools merge

Doing that, I got 215,834 exons, but every reference I saw mention something like 180.000 exons on human protein coding genes.

Besides that, the total base pairs of the exons I extracted is > 80Mb, and all human exome sequencing get about 30Mb.

Anyone can understand what’s wrong with the logic of extracting an exome from the genome?

(I saw other related posts but no one actually helped)