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Old 10-25-2016, 08:49 AM   #1
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Location: sf bay area

Join Date: Dec 2013
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Default Converting variant alleles back to reference in an alignment

Hi All,
I am trying to create a "normal reference" BAM file from a set of BAM files that are contaminated with tumor. I was thinking to merge the BAM files, call variants, and then go back and edit the reads - replacing the mutant alleles with reference. Maybe this is crazy, but I want to create a normal reference from these patients, so that I can use it to call somatic variants on the same patients post-relapse samples, for example, with MuTect.
Any ideas?
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