I am currently working with Level 1-3 TCGA data. I'm trying to redo the Copy Number Variation analysis that they did, getting a report of copy number losses and gains, as well as loss of heterozygosity reports. Every program I have tried reports a heatmap or other visualizations for these.
What I'd like to see is a program that spits out how many individuals have gains/losses on each chromosome arm, where I can set a threshold. Another thing that would be nice is one that can identify copy-number neutral LOH (where the allele difference plot has a line at +1 and -1, but nothing at 0...in other words, no heterozygotes in a region, but no change in copy number).
Anyone know of a program that does this for me, or am I stuck 1) going through samples one at a time or 2) creating code myself to quantify this?
Thanks in advance,