Open vinjlynch opened 2 months ago
Thank you for the question! Since GeneToCN is optimized for and validated on WGS data, it assumes a uniform coverage in the gene region and a single copy reference region to be able to compare the k-mer frequencies and estimate an accurate copy number. Considering the coverage variability and potential biases from the target-capture process, the copy number results may not be reliable using whole exome target-capture sequencing data (even if there are suitable single-copy reference regions sequenced, which might not always be the case, I would think). Unfortunately I don't have experience using this kind of data myself, so I am not familiar with typical coverage profiles. It would be interesting to look into it in the future to see if it would be possible to estimate copy numbers reliably.
Hi,
I'm curious if it is possible to use fastq files with reads from whole exome target-capture raw sequencing?
Thanks Vinny