How do I calculate the average coverage of genome?

[prs321]

Say if I have an ancestral strain, as well as 20 replicates. The 20 replicates are divided into 4 treatment groups, so 5 replicates per treatment group.

I have 4 .bam files for each treatment group containing 5 replicates per .bam file.

I also have the variant files.

How do I calculate the average coverage of the genome?

I'm confused on what file to use to calculate the average.

Do I use one of my treatment .bam files, a variant file, or the ancestral strain?

I have bedtools installed as well as genomecov, but I'm not sure how to obtain the average coverage value that I am looking for.

[mikep]

samtools idxstats will give you the number of mapped reads per reference, you can then divide this number by the length of the reference to get the coverage.

Do it for each bam file.