DEPTH IN GBS

Question

[Michelle Guerra]

Hi all! 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.

[Pierre Lindenbaum]

  -a           Output all positions (including zero depth)

what don't you understand here ?

[Michelle Guerra]

Is it important to consider zero positions?

[Pierre Lindenbaum]

yes. but there are better tools than samtools depth to get the depth. e.g: mosdepth.

Answer 1

[Huiyang]

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.

[Michelle Guerra]

For each position, Thanks, I will search PanDepth