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
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