I don't know enough about genomics files. I have a human tumor sample of bam, which used bwa and sambamba aglined and targged with duplicated reads. I used the below of commands converting the bam file to a wig file required by HMMcopy.

/path/hmmcopy_utils/bin/readCounter --window 1000000 --quality 20 \ --chromosome "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,X,Y" \ /path/data/CTC.final.bam > /path/data/CTC.wig

But I don't know how to get the gc.wig required by HMMcopy. How can I get a GC file?

By the way, I think I can use the example of map.wig in HMMcopy package as my datainput of map.wig. Is this ok?

mfile <- system.file("extdata", "map.wig", package = "HMMcopy")

I'd appreciate it if anyone can give me some advice.