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Do bams output by realignment and recalibration steps contain all information from input bam?

Hi,

My understanding is that a bam file output from the GATK after realigning indels and recalibrating bases will contain all of the original bam's information (along with new information), except for reads which GATK states that it has filtered at the end of these processes. Is this correct? Thank you in advance.

Best,
Monica

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