Hi GATK Team,
I'm following the CNV workflow: Sensitively detect copy ratio alterations and allelic segments.
I ran step 1-4 with my own WGS 30x samples and a 7 sample PON to test against my tumor samples. All bam files were preprocessed by FireCloud workflow. I'm using hg38. No error messages at the end. my GATK is 4.0.8.1
At the end of step 4, I have a few questions:
- for one patient, the standardize and denoise plots disagree with each other not only one cell clone but different ones, but only this patient.
I can't post markdown links to my images, please see attachment.
1. Standardized plot shows increase at X but denoised plot shows decrease. How did this happen? Is this related to my sample itself, the PON components(7) or calling algorithm?
2. Like the two sample plots above, some samples give me a smooth line of CNV ratio and some other samples have more noise. How did the difference occur and how can I improve it?
Thank you!
Le