verifyBamID seems to be the most popular tool for estimating the levels of contamination in WGS data. It calculates the FREEMIX and CHIPMIX* scores for provided BAM libraries. Unfortunately, the tool is slightly outdated and doesn't support CRAM inputs. The tool doesn't use HTSlib, so recompiling verifyBamID with a newer version of HTSlib is not a solution. Is there an alternative tool that calculates FREEMIX/CHIPMIX and supports CRAM input files?

* if external genotypes are available.