I am using CNVkit batch function to process a number of WES tumor samples from Breast Cancer. I know that all my samples are from female patients, yet the CNVkit log tells me that some of the samples are assumed male. As a result there is a loss of X in these samples.
How can i fix that? I am worried that this indicates a larger problem with the data. The reads were aligned with BWA, reduplicated and recalibrate as per the BROAD best practices recommendations.