briefly, in a current collaboration project, i have performed variant calling analysis on cancer whole exome sequencing data on a small number of 4 patients with small cell lung cancer (Circulating tumor cells sample, biopsy cancer sample and the relative peripheral blood normal sample). Now, except the completed somatic variant calling with GATK4 and mutect2 updated pipeline, I have also performed the suggested GATK2 pipeline for copy number alteration events identification. Currently, my goal is to examine specifically the CTC samples to estimate their relative tumor purity.
The notion for this, is that our collaborators have established a novel biological protocol for the isolation of circulating tumor cells and the subsequent creation of liquid biopsies-thus, an additional estimation of purity (even from the computational perspective) would strengthen the hypothesis if the isolated cells are mainly tumorigenic, or they present contamination with other cell populations (which is expected but the percentage matters..). Thus, is there a tool or pipeline you would suggest for estimating the tumor purity, based on my project description and nature of samples ?
Thank you in advance for your time and consideration on this matter !!