How to get the coverage of whole gene in exome sequencing data

Question

[MAPK]

I can get the allelic depth of any SNP by using pile-up. However, I need to get the coverage of gene in the exome sequence (preferably with number of reads with REF allele and number of reads with ALT alleles). I have some genes where variants are not called by GATK and I want to check if that is because of low coverage and not because they do not exist. Is there a way to do this using BAM files rather than going through each individual gene using IGV?

Answer 1

[Sean Davis]

See samtools bedcov or samtools depth.

[MAPK]

Thanks a lot!

Answer 2

[GenoMax]

Calculate Per Exon/Per Gene Coverage