I use Mutect to find somatic mutations in multiple tumor samples (to be used in clonality analysis). I don't get the readcounts if the caller did not identify a somatic mutation in a sample. I'm using bam-readcount to fill in the empty values after merging Mutect results from different samples. Where I have values from both tools, the readcounts are lower in the Mutect results. Is there a way to use bam-readcount in a way to substitute for missing Mutect values?