Downsampling method of ichorCNA benchmarking

[yuanzhao0502]

I have a question about your benchmarking work. In your paper, you downsampled to the number of reads required to reach exactly 0.01, 0.02, …, 0.09, 0.10 tumor fraction at 0.1× coverage. In the equation, you use the reads number to control how much percentage to downsampled. I am wondering you do the downsampling the bam file by Picard or just use reads number which detected by hmmcopy to multiply the percentage. Because when I use Picard to downsample a bam file, I found it is difficult to control the final reads number very accurate. After that when I use ichorCNA to detect tumor purity, the result is not good. I guess the problem is that the downsampling part is not randomly enough to keep the tumor purity as our expectations. Could you give me some suggestions?

[gavinha]

Hi @yuanzhao0502

I used Picard DownSampleSam. I also made sure to downsample a BAM that has duplicates removed. The readCounter tool in the ichorCNA pipeline ignores duplicates and sampling duplicate reads was an issue.

Hope this helps. Gavin