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?
Many callers do some filtering of reads first (by base quality, by mapping quality, maybe even local realignment) and report only counts from reads that pass. bam-readcount, by default, outputs "raw" counts. You may or may not be able to mimic those Mutect settings with bam-readcount parameters.
This problem is compounded when merging the output from different variant callers, and there is no "perfect" solution.