I have a big list of genes and I found the uncovered regions (0X, WES data). The point is that I have the uncovered genome coordinates but I do not know the related gene names of those coordinates...
In "Genome Browser -> Tools -> Table Browser": I take the coordinates of all exons of the gene list... and I use "bcftools sort" and "bcftools merge" to have the final bed list to use with "samtools dept". At he end I will have the base coverage for all bases of my intervals.
With which tool / command / file I can give to each coordinate the gene name?
Example of what I want:
CHR START COV GENE chr1 1025 0 CFTR
I only have the first 3 columns and I need also the last one.