Question: copyCat error (copyCat2)
0
gravatar for Jackie
4.5 years ago by
Jackie70
United States
Jackie70 wrote:

Hi, I am trying to use copyCat to call somatic CNVs on a set of tumor-normal paired whole exome sequencing data. Seems there isn't a comprehensive manual on how to use it, and the only command example I could get is from here: https://github.com/chrisamiller/copycat

The R command I used was: 

runPairedSampleAnalysis(annotationDirectory="~/annotations/copyCat/hg19/",
                    outputDirectory="ccout",
                    normal="normal_bam_window",
                    tumor="tumor_bam_window",
                    inputType="bins",
                    maxCores=2,
                    binSize=0, 
                    perLibrary=1, 
                    perReadLength=1, 
                    verbose=TRUE,
                    minWidth=3, 
                    minMapability=0.6, 
                    dumpBins=TRUE,
                    doGcCorrection=TRUE,
                    samtoolsFileFormat="unknown", 
                    purity=1,
                    normalSamtoolsFile="normal_mpileup",
                    tumorSamtoolsFile="tumor_mpileup")  

 

But it keeps throwing these messages:

[1] "inferred bin size:  1000"

[1] "WARNING: bins file wasn't created with per-library option, will not perform per-library correction"

[1] "WARNING: bins file wasn't created with per-read-length option, will not perform per-read-length correction"

[1] "Can't infer read length from window file headers"

[1] "and read length was not specified in setParams()"

[1] "correct one of these to proceed"

Error in getWindowBins(rdo) : 

 

The 'normal_bam_window' and 'tumor_bam_window' are text files that have the read-count information for each bin (i.e., 1000bp in this case), that are generated by applying 'bam-window' on the bam file.

Can anyone with similar experience help on this?

Also, I heard there is another version of copyCat, which is called copyCat2, but I can't find 'copyCat2' anywhere, does anyone know where to download copyCat2?

Thanks,

J

 

 

 

 

 

cnv copycat2 copycat wes • 1.6k views
ADD COMMENTlink modified 3.6 years ago by hongen.hugo.xu0 • written 4.5 years ago by Jackie70

Can anyone help on this?

ADD REPLYlink written 4.5 years ago by Jackie70
0
gravatar for hongen.hugo.xu
3.6 years ago by
Germany
hongen.hugo.xu0 wrote:

Did you solve your problem? bam-window has parameters -l and -r, you need to specify them when you run bam-window.

ADD COMMENTlink written 3.6 years ago by hongen.hugo.xu0
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