I've been trying to use cn.mops to identify copy number variants among 10 individual of my (non-human) study species. Each individual was subjected to Illumina whole-genome sequencing, and the reads were mapped to the reference using Bowtie2. I have mostly been following the cn.mops manual:
All of this went through without error. However, when I try to view the data (with cnvs or cnvr), everything in the "logical" column, which I believe should contain the estimates for copy number simply says "<NA>" What could be the cause of this?
I am able to view plots of the data with plot and segplot just fine.