Frac. CNA Subclonal: 0.99

[Jingjiao-ma]

hello

--maxFracCNASubclone=MAXFRACCNASUBCLONE Exclude solutions with fraction of subclonal events greater than this value. Default: [0.7]

The Frac. CNA Subclonal: 0.99 of my result is 0.99. My window is 1000000, the cfDNA sample depth is 5X. why?

thank you best P2557225160920_genomeWide.pdf P2557225160920.params.txt

P2557225160920.cna.seg.txt

[gavinha]

Hi @JJMaggie

This is the only solution that is produced so it will select it by default. You should consider generating more solutions so that either you or ichorCNA can try to select the best one.

You can do this by using multiple values for --normal and --ploidy Please see the example in the README here: https://github.com/broadinstitute/ichorCNA/tree/master/scripts

If you used Snakemake, you can also set this in the config.yaml file for fields ichorCNA_normal and ichorCNA_ploidy. Please refer to the README here: https://github.com/broadinstitute/ichorCNA/wiki/SnakeMake-pipeline-for-ichorCNA

Hope this helps. Best, Gavin