Read depth interval comparison

Question

[rbronste]

I was wondering about a good method to compare read depth at specific positions (bed file intervals) between two bam files and get as an output the depth across both bam files next to each interval in question? Thanks!

Answer 1

[Pierre Lindenbaum]

samtools depth -b in.bed 1.bam 2.bam 3.bam 4.bam