Hello,
I am interested in inferring clonal evolution using somatic variants called by Mutect2. One way to infer is by tracking VAF (variant allele fraction) of somatic variants in multiple time points and clustering.
One challenge in using Mutect2 calls is its difficulty to compute VAFs especially for indel, because some variants are called using local assembly in a subset of time points. Allele counting in time points where the variant is not called is tricky. Thus, I usually limit variants to SNPs which is less hard to count. But some cohorts don't carry many somatic variants and I believe it would be helped by joint calling. Does it make sense?
Would you consider implementing joint calling for Mutect2 like Haplotypecaller?
(Image credit: https://github.com/chrisamiller/fishplot)