Test-drive the GATK tools and Best Practices pipelines on Terra
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Is there any "pre copy number" value in the processing?
Dear Genome STRiP users,
I completed the SVCNVDiscovery process to a certain cohort, and also calculate the copy number by other software such as Lumpy. But when I compare these two copy number results, I found some samples with weird copy number values.
|samples||lumpy CN||GS CN|
It is hard to figure out the conversion between the continuous CN from lumpy to the discrete CN from GS. I am wondering if in Genome STRiP, it also generate continuous CNs and then discretize them to the final discrete value. If so, where can I get the "pre" value of the final discrete CNs or can I output this kind of "pre" value? Thank you very much.