I need help, I have files from GBS and need to know your depth of files. I know it is necessary “samtools depth”, but I do not know the difference between using Flags (-a) or not using it. Because it is important to consider zero positions. You help me.
I'm not quite sure if you are looking for depth data for each position (including zero positions) or specific regions. If you have a large amount of GBS data and wish to calculate the coverage or depth for each sample, you can try PanDepth, a specialized tool for coverage and depth calculation that supports both short reads and long reads.