Hi all,

I’m working on some tumor samples and need some advice on interpreting results. I'm using GATK’s CalculateContamination tool to estimate the level of normal DNA present in the samples, and I’m assuming that 1 - contamination gives me the tumor purity (useful for cnvkit). However, I’m unsure if this directly correlates to tumor cellularity.

Interestingly, in some of my samples, I observe very low contamination (suggesting high tumor purity), but actual tumor cellularity is also quite low. I'm trying to understand why this discrepancy might exist.

Has anyone encountered similar situations or have insights on how to interpret these metrics effectively? Also for cnvkit which of the two metric should I use?

Thanks in advance!