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Can we run GATK 4 MuTect2 on indel realigned files?
I had used the old GATK 3 pipeline for preparing BAM files for germline variants. The pipeline included indel realignment, which was part of the Best Practice Pipeline back then.
Those BAM files include normal and tumor samples. Now I'd like to use the latest GATK 4 MuTect 2 for running a normal/tumor somatic variant calling. However, those BAM files had been indel realigned, but the latest GATK 4 doesn't require indel realignment?
Would giving indel realigned BAM files (from GATK 3) for GATK 4 MuTect2 create bias? In general, can I reuse the BAM files prepared by GATK 3 (e.g. marking duplicates) for the new GATK 4 MuTect2 tool?