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Mutect with multiple bams or single bams
I've a general question about the input files that MuTect tool requires and if there are differences if I use one method or another, let me explain. I have 8 bam files (4 normal and 4 tumor, matched one to one). Questions:
1) How should I call MuTect tool? Should I ran mutect 4 times (one per sample:normal-tumor)? Or it is better if I call MuTect with the 4 normal bams as "normal" and the 4 tumor bams as "tumor" all in one run (is this possible and if it is, how? just like in GATK?).
2) Regarding the reads groups on bam files... should I change the reads group to "tumor" or "normal", or it is not necessary? I mean: in the command line:
-I:normal sample1_N.bam \
-I:tumor sample1_T.bam \
Does MuTect detect that sample1_T.bam is a tumor bam because it is specified "-I:tumor" or because the read group is "tumor"?
3) Is better to create first a "panel of normals" using the 4 normal bams, and then run MuTect giving as input the vcf file? What would be the difference between running with/without the panel?
I hope I've explained myself.
Thank in advance.