Im using cn.MOPS for detecting CNVs in multiple WGS samples, however i got some questions concerning the interpretation of the output:
- When using returnPosterior=TRUE should i have an additional column with a posteroir probability value or is the output filtered according to the latter? I havent a posterior probability column, and here is the command i have used (with no error):
resCNMOPS <- cn.mops(bamDataRanges, returnPosterior = TRUE) resCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)
2. I have a coverage of about 10X and a total of 40 samples, which threshold would you suggest to use to select final cnvr (group together CN0-1 as loss and CN3-8 as gain)? I read that i can play around with WL although the software it does estimate it from the data, which is best given that i dont have a training set? Moreover, in another post you talked about sI/NI value which i dont have in my final tables, where can i retrieve it?
3. These 40 samples represent two populations, would you recommend to run cn.mops per population?
I really like cn.mops and hope to get some more advice from you.
Thanks a lot in advance for your time and support,