I'm using the sciClone R package and got very exciting data with that! Now I am wondering if anyone has experience in attributing non-integer values to the copynumber segments in which the measured VAFs are located. Given that I am confident to measure an accurate copynumber value of 1.5 (meaning 50% of cells are deleted), the VAFs of variants in this segment would need to be corrected differently than VAFs in segments with CN=1 or CN=3. As far as I understand, VAFs in segments with copy numbers close to integer values get attributed those integer values, while VAFs in segments with intermediate CN (eg 1.5) will be dropped, although they would nicely contribute to specific mutation clusters, especially of they consist of very few mutations. I'd be glad to hear some opinions on that!