Tumor Purity argument for Somatic CNA's

[Yash Prasad]

Hi There

I have a question regarding how the tumor purity values are parsed for somatic CNA analysis.
I understand its by using '-t'. I don't understand whether it takes it as a percentage or decimal.

For example if the purity is 88%, it shuld be introduced as "-t 88" or "-t 0.88"

Thanks for the help!

[Tobias Rausch]

The -t command-line parameter is indeed somewhat related to tumor purity, ploidy and subclonality. To have maximum flexibility, I so far opted for a simple command-line parameter that determines the min. copy-number shift for the segmentation and somatic classification. For instance, for a diploid tumor with 80% tumor purity, a clonal genomic rearrangement of copy-number 3 would be observed at CN 2.8 = 0.8 * 3 + 0.2 * 2 so you can put a very stringent threshold of -t 0.5. However, for a tetraploid tumor with 30% tumor purity, a clonal genomic rearrangement of copy-number 5 would be observed at CN 4.3 = 0.3 * 5 + 0.7 * 4 so you need to use a very lenient cutoff such as -t 0.2 to detect such a shift in copy-number from 4 to 5.

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