ichorCNA copy number ratio in the cna.seg file differs from the genome wide plot

[manasa-surakala]

Hi, When there is no normal wig supplied, the minimum log2 ratio is going upto -6 in cna.seg file but that value is not showing up in the plots. Is there any limitation in the plots shown (-2 to 2) ? Also, when I run including a normal wig, then the tumor fractions change a lot. Eg. for one sample it changed from 0.3 to 0. Please comment on this. Thanks, Manasa

[gavinha]

Hi,

Are you using ichorCNA for whole genome or whole exome sequencing data? If it's exome, then you will definitely need a matched normal. This can have a major effect on your results. If it's genome, then you a normal is not required. However, if you do use a matched normal, you should expect cleaner signals and profiles. Is this the case? Do you have examples you are willing to share? You can also send to me privately at [email protected].

You can change the plotting y-axis limits by using --plotYLim "c(-6,6)" when running runIchorCNA.R. If you are using the snakemake pipeline then modify this line https://github.com/broadinstitute/ichorCNA/blob/05519bf02d4ae6c949b89551152cb107f86fdcb2/scripts/snakemake/config/config.yaml#L42