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:
 "inferred bin size: 1000"
 "WARNING: bins file wasn't created with per-library option, will not perform per-library correction"
 "WARNING: bins file wasn't created with per-read-length option, will not perform per-read-length correction"
 "Can't infer read length from window file headers"
 "and read length was not specified in setParams()"
 "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?