Recent i am doing CNV analysis, i find a strange thing:
1.when using whole data (after removed dup, for tumor and its control), the copy number value is accurate;
2.but when downsample different fq reads from the whole fq for a certain sample (I just downsample the tumor's fq, and do not downsample its control's fq), the copy number is different from the whole fq data result, and the smaller downSample fq reads, the more difference between whole data cnv result and downsample cnv results.
Anyone ever encountered this problem? I am now very confused by CNV downsample analysis. thanks for your help.