Identifying coverage differences in two WGS platforms

Question

[mg]

I am comparing data from two whole genome sequencing platforms and would like to find out if one platform covers certain regions better than others (and why)? Would you recommend any tool(s) to do such comparison?

Also, one platform used hg19 as reference sequence as reference genome, whereas the other used GRCh37. My understanding is there should not be any difference due to this. Am I correct, or is there any pitfalls I need to be cautious about?

Answer 1

[ATpoint]

I would create a bedGraph/bigwig and then extract the mean (or per base) coverage of the respective regions. Options are BEDtools genomecov, deeptools bamCoverage, SAMtools depth or, relatively new and wickedly fast, mosdepth. That will answer the "if" but not the "why". For the "why" you'll need to provide some more details on which platforms you compare.