I'm analysing some human CLL data (cancer, whole exome), and when running fastqc to see how data are I observe all samples do show a bimodal GC content. Generally the only warn shown by Fastqc happens for the GC module, the other normally are good.
I have runned the fastq_screen unly against human genome having a 80% only one hit reads, 18% having multiple hits and about 0.6% not mapping against human, this is making me thinking that no contamination is present in the samples.
After some thoutghs I do not know why samples do show this kind of distribution.
Thanks for your time.