What tools can I use to calculate sequencing depth and sequencing coverage for ddRADseq data

Question

[jingjin2203]

Hi All, I have some ddRADseq data, I would like to know what are some tools that I can use to calculate the sequencing depth (the number of times that each base has been sequenced) and the sequencing coverage (the percentage of the whole genome that has been sequenced). Hope to get some advice here. Thanks in advance!

Answer 1

[GouthamAtla]

You can use genomeCoverageBed to get the coverage at each base in the genome and also later you can calculate the percentage of genome sequenced.

If you are using the stacks pipeline, you could also calculate the coverage per loci, number of loci sequenced etc.