I need some suggestions regarding CNV analysis. I want to know CNVs which I have found in normal/tumor pair , to what extent they are overlapping with CNVs from normal/ipsc( induced pluripotent stem cell derived from tumor). To this I extracted the CNVs regions from both normal/tumor( hereafter reported as tumor.bed) and normal/ipsc (ipsc.bed) in form of bedfiles. Now if I have to report the overlap of regions or features that between tumor.bed and ipsc.bed which option of intersect.bed should I use? I have 121 rows for tumor.bed and 199 for ipsc.bed. My tumor.bed file and ipsc.bed file only contains chr#, start and end coordinates.
I want to know the CNVs that I found in tumor.bed to what extent they are conserved in ipsc.bed. I am providing the below bedtools command. Which should I use to get this information?
bedtools intersect -a tumor.bed -b ipsc.bed -wa -wb -f 1.0 | wc -l
45 ( this shows features of tumor.bed file that overlaps 100% with ipsc.bed) . This is similiar to
bedtools intersect -a tumor.bed -b ipsc.bed -u -f 1.0 | wc -l
however if I do just
bedtools intersect -a tumor.bed -b ipsc.bed -wa -wb | wc -l
bedtools intersect -a tumor.bed -b ipsc.bed -u | wc -l
So I am bit confused which should be the ideal command to use in my case. My goal is to see if CNVs found in tumor remain conserved in ipsc or not? I would like to have some suggestions