I'm using cn.mops to detect CNVs from Targeted DNA Sequencing data by "TruSight One Sequencing Panel from Illumina" investigated for one patient and one control samples, on an Illumina MiSeq sequencer with 150 bp paired-end run.
By running the algorithm with the referencecn.mops function, it results #GRanges object with 67 ranges.
Then, by verifying, the resulting CNVs with the coverage of the enriched regions in the raw data,
I found that several detected CNVs aren't included in the targeted regions enriched by the panel!!
Please, How can you explain that?
Find below my code, what am I doing wrong?
BAMFiles <- list.files(pattern=".bam$")
bamDataRanges<-getReadCountsFromBAM(BAMFiles,sampleNames=paste("Sample",2:3), refSeqName= refSeqName,mode="paired",WL=5000)
case.ctrl2<-referencecn.mops(cases=bamDataRanges[,3],controls=bamDataRanges[,2]) case.ctrl2.ICN <- calcIntegerCopyNumbers(case.ctrl2)