Confirm if a genome position falls into a coding exon

Question

[Lila M]

Good morning,

I do have few human positions of interest and I want to check if they fall inside a coding exon. I know genome browser (https://genome.ucsc.edu/cgi-bin/hgGateway) is very useful for visualization, but I am more interesting in identify different overlaps. \Would it be possible to download it from somewhere? Thank you!

[GenoMax]

Something along these lines: intersect snp and exon coordinates

Answer 1

[Pierre Lindenbaum]

get a gtf, convert to bed, sort and merge with bcftools merge. e.g: awk -F '\t' '($3=="exon") {printf("%s\t%d\t%d\n",$1,int($4)-1,$5);}' in.gtf

put your position(s) in a bed and sort

use bedtools intersect.

[Lila M]

Thanks both. Will be $3=="exon" enough to select only the 'coding' exons (and to exclude any non-coding exon)?

[Pierre Lindenbaum]

$3=="CDS"

?