genome to exome

Question

[storm1907]

Hello, I would like to convert GRCh38 genome reference file to GRCh38 exome reference file. I need to get GRCh38 exome file as control, but I cannot find any appropriate database. Exome variant server offers liftover to GRCh38, but this is not best approach, because a lot of variants are lost in such way

Is genome conversion to exome possible and has anybody done that? I guess, Bedtools can be used, but I am not sure

[Pierre Lindenbaum]

GRCh38 genome reference file to GRCh38 exome reference file.

what does it mean ? what would the be content of the fasta file.

[Ram]

Your title and tag make next to no sense, OP. Please use a sensible (clear, concise, to the point) title and tags that are subject matter related, not something so broad that I could replace it with "bioinformatics question" and it would be as close to what you want as your current title.

[GenoMax]

Is genome conversion to exome possible and has anybody done that?

While that is informatically possible to do, methods used for WGS/WES are different on experimental side. Keep that in mind as you look at published data.

Answer 1

[ATpoint]

GRCh38 GTF files e.g. from Gencode, extract exon coordinates and then use bedtools getfasta based on the genome fasta to get the sequences.