I'm not familiar enough with genomics files. I have a human tumor sample in BAM format (CTC.final.bam), which was aligned and tagged with duplicated reads using BWA and Sambamba. I used the following commands to convert 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?

The R package tutorial below explains the source of the gc and map files, but I'm still unsure where to download the mappability file and gc file.

The section of the vignette that is directly above the one you quote says that you can use the HMMcopy utils to do all three things. And you apparently already have the HMMcopy utils, so if I were you, I would use gcCounter and mapCounter to generate what you need.