I am currently running samtools depth on several bam files, after updating to the latest version of samtools v1.21 I found that the results differ from the previous version I was using v1.19.

I run the exact same command for the same file, overlaps by pair-reads was counted as 1 with the -s flag

samtools depth -@ 15 -s -o depth.out -g DUP bam.file

v1.21 consistently has higher or equal depth for all positions than v1.19, (checked with a script for all positions) I was wondering why this was the case and how the 2 versions differ in the way they count the read depth.