some days ago I got helped using varscan copynumber for a paired samples (tumor, normal)
And of course the results look like this:
chrom chr_start chr_stop num_positions normal_depth tumor_depth log2_ratio chr1 14904 14973 70 17.9 3.2 -2.497 chr1 16770 16834 65 21.9 13.5 -0.694 chr1 63298 63335 38 11.7 3.9 -1.582 chr1 63632 63700 69 20.3 8.7 -1.225 chr1 135158 135188 31 3.8 11.5 1.605 chr1 567576 567609 34 16.8 1.4 -3.600
Dan Koboldt recommended the R package "DNAcopy". But I don't know how to work with it. I don't know what the meaning of the examples data (coriell) is. And also not, what to put into the functions from the varscan resulting data.
Maybe one of you has some hints for me or maybe another solution?
With all the best,
Maybe there is also a way to view this in IGV like this?! But again, what data to input? Format? Found a small description for the SNP format here (got the link from the IGV FAQ), but I don't get in touch with it. So maybe it's possible to convert the data?