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GATK Workflow for Cancer
I am new to Bioinformatics, and would like some advice on changes to the GATK workflow for cancer. I was told that the cancer workflow is different, and see that several different tools are available.
I have Exome data from tumor and normal. I have aligned them, and have BAM files for each sample. I am interested in identifying somatic variants.
The current workflow as I understand it is:
-(Non-GATK) Picard Mark Duplicates or Samtools roundup
-Indel Realignment (Realigner TargetCreator + Indel Realigner)
-Base Quality Score Reacalibration (Base Recalibrator + PrintReads)
-Annotation using Oncotator (?)
-MuTect (identify somatic mutations)
My questions are:
1. Is the above workflow reasonable/correct for what I'm trying to do?
2. Is there any difference running samples one pair at a time, or running them all together? (I have 57 pairs. Should I do 57 runs of normal-tumor pairs, or 1 run of all 57 pairs?)