Calculating Sequencing Depth Of A Genomic Region

Question

[User 1933]

In an whole-exome study project, I need to calculate the sequencing depth for a given set of genes. It seems DepthOfCoverage from GATK can do this for me. However, I am curious if I can get the similar information from the VCF file ? Alternatively is there any other tool I can use ?

[Biomonika (Noolean)]

As far as I know, VCF file will provide you depth only at the position of the variant. It depends if you are interested in depth at variants, average depth across the gene or in depth for every position in the gene. If the last one is your case, you can use "samtools depth" over the bam file (alignment file of reads over reference).

Answer 1

[Alex Paciorkowski]

GATK DepthOfCoverage will give you want you want, but it takes bam files.

Also, read this, it's a nice discussion of using bedtools as well.

I wouldn't calculate my read depth across the target just using a vcf, since that file only includes your variant calls.