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Do alignment differences affect a lot with GATK Haploytype Caller?
We find with the same sample aligned with different version of bwa thus with different bam files(We test the two bam files with deeptools, and find the two are quite different), we may get very similar variant result with gatk germline pipeline, is this due to that the haplotypecaller is more tolerant with the alignment file since it will do the realignment itself or we just ignore some other factors that will lead to this result？