Calculate coverage per gene

Question

[anii]

Hi everyone,

I have bed file, bam file of human exome data and i wish to calculate the coverage per gene. Are there any suggestions on how i should calculate the coverage per gene?

[Pierre Lindenbaum]

How to calculate average coverage for all genes

Answer 1

[iraun]

I like Mosdepth for coverage related issues.

[anii]

I have used the mosdepth but it in the output in showing me the coverage of whole exons of genes. so how i can combine the coverage and get the coverage by gene wise not an exon wise?