copyCat error (copyCat2)

Question

[Jackie]

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

[Jackie]

Can anyone help on this?

Answer 1

[hongen.hugo.xu]

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