cn.mops settings for calling CNVs in MIP data
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Entering edit mode
7.2 years ago

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

cancer cn.mops mip • 2.4k views
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I am facing the same problem with my exome data. Have you found a solution yet?

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