Kurt-Hetrick
commented
1 year ago looks promising. a tumor sample that had 26% freemix was 2% for gatk, so maybe in this use case. wouldn't expect it to help with bacterial or cdna contamination. it's only supposed to help with tumor contaminated by normal and not normal contaminated by tumor, but it's better than what we had before.
can it differentiate between verifybamid estimate for tumor cellularity. i.e. for normal sample or a normal sample contaminated by another normal sample, will verifybamid and calculatecontamination give the same result, but the result for tumor sample will be significantly different for the two samples.