Question: bam-readcount values are higher than Mutect results
gravatar for sey
3.6 years ago by
sey10 wrote:

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?

bam-readcount • 925 views
ADD COMMENTlink modified 3.6 years ago by Chris Miller21k • written 3.6 years ago by sey10
gravatar for Chris Miller
3.6 years ago by
Chris Miller21k
Washington University in St. Louis, MO
Chris Miller21k wrote:

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.

ADD COMMENTlink written 3.6 years ago by Chris Miller21k
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