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Dear GATK team,
I have noticed that sometimes, when I run IndelRealigner independently on a tumor BAM file and its matching normal BAM file, I get different haplotypes, leading to false somatic variant or indel calls. Is there a way to ensure that both BAM files are realigned the same way ? For instance, merging both BAM files together, running IndelRealigner and splitting resulting BAM file by read group ?