Titan reporting very short CNVs

[d-henness]

I'm running PhyloWGS with Titan and I'm getting an error that says I have CNVs with the same start and end locations. When I look as the segs.txt file for that sample, I see that there are indeed several CNVs with very short lengths. This seems strange to me, can anyone suggest a reason this might be happening?

[gavinha]

Hi @d-henness

My guess is that you have some noisy outliers that are being called as individual segments. You can either exclude these segments prior to PhyloWGS.

You can also try to re-run TITAN using parameters that may help to smooth over these data points. Increase the value for the argument txnExpLen. https://github.com/gavinha/TitanCNA/blob/c3061eaa437785ec2ca8618c7d24603c4df9eb14/scripts/R_scripts/titanCNA.R#L61-L62

If you are using the snakemake workflow, you can adjust the values in config.yaml https://github.com/gavinha/TitanCNA/blob/c3061eaa437785ec2ca8618c7d24603c4df9eb14/scripts/snakemake/config/config.yaml#L77