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?
thanks
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?
thanks