We are comparing two library prep kits: Nextera DNA Flex Library Prep and TruSeq DNA PCR-Free Library Prep for whole genome sequencing. The purpose of this comparison is to predict how will they affect the result of CNV calling.
So we whole-genome-sequenced the same sample prepped with either of the two preps, mapped them to the reference genome with bwa mem.
Now we have the general mapping statistics but that is not enough. To evaluate how CNV calling will be affected, our fist idea is to evaluate the eveness of coverage, but don't know to evaluate that properly.
Any ideas or existing tools to compare the coverage?