I would like to compare mutational signatures1 in patients from different studies, however some studies are based on exome seq (i.e. ~20,000 coding variants) and some are from whole genome seq (i.e. ~22,000 coding variants) - is there a way to 'downsample' WGS data to better reflect WES data and effectively 'ignore' the coordinates of those ~2000 coding variants in the VCF files?
1Alexandrov, L.B., Kim, J., Haradhvala, N.J., Huang, M.N., Ng, A.W.T., Wu, Y., Boot, A., Covington, K.R., Gordenin, D.A., Bergstrom, E.N. and Islam, S.A., 2020. The repertoire of mutational signatures in human cancer. Nature, 578(7793), pp.94-101.