Entering edit mode
18 days ago
Mateo
•
0
I'm trying CNVkit on FFPE targeted panel NGS data with 300 genes. I'm in the process of making a reference.cnn from 50 tumor samples.
I read the doc quickstart (https://cnvkit.readthedocs.io/en/stable/quickstart.html) and it said "Inspect the coverages of all samples with the metrics command, eliminating any poor-quality samples and choosing a larger or smaller antitarget bin size if necessary". After running 'metrics' I got these results:
sample segments stdev mad iqr bivar
TM24-0743_tumor.targetcoverage.cnn - 0.5223 0.382844 0.519745 0.418463
TM24-0748_tumor.targetcoverage.cnn - 0.574451 0.371302 0.50387 0.421322
TM24-0755_tumor.targetcoverage.cnn - 0.436836 0.284481 0.3854 0.326914
...
sample segments stdev mad iqr bivar
TM24-0743_tumor.antitargetcoverage.cnn - 4.34981 0.422786 0.571706 0.391274
TM24-0748_tumor.antitargetcoverage.cnn - 3.89586 0.731915 0.987979 0.680454
TM24-0755_tumor.antitargetcoverage.cnn - 4.00702 0.642974 0.869162 0.608133
...
My question is:
- what is a normal range for these metrics?
- my antitargetcoverage metrics look like they are more variable than targetcoverage - is this concerning? Should I try "choosing a larger or smaller antitarget bin size"?
Thanks in advance