Dear all,

Please may I ask for an advice regarding the use of cn.MOPS BioC package (http://bioconductor.org/packages/release/bioc/html/cn.mops.html) on WES data containing TUMOR-GERMLINE paired samples. I wrote the following piece of R code (below) -- please would you let me know if it looks fine, or if it needs any modifications.

segments <- read.table("hg38_refFlat.longest.isoform",sep="\t",as.is=TRUE)

gr <- GRanges(segments[,1],IRanges(segments[,2],segments[,3]))

TUMOR <- "zzz2.bam"

GERMLINE <- "zzz1.bam"

tumor <- getSegmentReadCountsFromBAM(TUMOR, GR=gr, parallel=1)

normal <- getSegmentReadCountsFromBAM(GERMLINE, GR=gr, parallel=1)

X <- tumor

values(X) <- cbind(values(tumor),values(normal))

head(X)

resCNMOPS <- exomecn.mops(X)

resCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)

-- bogdan