cn.mops settings for calling CNVs in MIP data

Question

[koenhendriks89]

Hello everyone,

I'm analyzing cancer samples sequenced with Molecular Inversion Probes (MIPs) which contain cnv's in the BRCA1 gene.

Since cn.mops is used to analyze WES data I want try if the program is able to call CNVs in my MIP data.

I'm now using the following code to run the program.

library(cn.mops)

pdf("cn_mops_plot.pdf")

BAMFiles <- as.matrix(read.table('/home/koen/bam_filelist_cn_mops.txt'))

#segments <- read.table("/home/koen/cnv_tool_comparison/reference_files/BRCA_1_2_new_mip_panel_sorted_merged_only_normal_mips.bed",sep="\t",as.is=TRUE)
segments <- read.table("/home/koen/cnv_tool_comparison/reference_files/BRCA1_2_new_mip_panel_sorted_no_snpmips_non_overlapping_no_chr22.bed",sep="\t",as.is=TRUE)

gr <- GRanges(segments[,1],IRanges(segments[,2]-30,segments[,3]+30))
gr <- reduce(gr)
X <- getSegmentReadCountsFromBAM(BAMFiles,GR=gr,mode="paired",parallel=12)
resCNMOPS <- exomecn.mops(X,parallel=12)
resCNMOPS <- calcIntegerCopyNumbers(resCNMOPS)

plot(resCNMOPS,which=1)
dev.off()

It fails however with the following output:

Normalizing...
Starting local modeling, please be patient...
Reference sequence:  chr13
Reference sequence:  chr17
Starting segmentation algorithm...
Using "fastseg" for segmentation.
No CNVs detected. Try changing "normalization", "priorImpact" or "thresholds".
Warning message:
In cn.mops(input = input, I = I, classes = classes, priorImpact = priorImpact,  :
  Normalization might not be applicable for this small number of segments.
Error in calcIntegerCopyNumbers(resCNMOPS) :
  No CNV regions in result object. Rerun cn.mops with different parameters!
Calls: calcIntegerCopyNumbers -> calcIntegerCopyNumbers
Execution halted

Can someone point me in the right direction about which settings to use?

Thank you very much for your help!

Koen

[eva]

I am facing the same problem with my exome data. Have you found a solution yet?