Hi,
To your first question, yes, we had a major pipeline update in 23Q4 and removed all of the silent mutations, among others. Please refer to our documentation on the mutation pipeline for more details.
To your second question, in 23Q4 we started masking genes that fall in segmentally duplicated/short repeat regions in our copy number matrix. This section of our 23Q4 release announcement describes this change.
Thanks,
Simone
