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.
Thank you for the clarification. The heatmap function is very useful and if it doesn't rely on sample gender that is good enough for our purposes. I will implement the -g option for the export function.