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When doing an indel realignment with GATK, the 'MD' field in the SAM/BAM record gets dropped for realigned reads. Is it possible to recompute them directly with GATK? I know that 'samtools calmd' does this, but are there alternative options?
No, that's not possible with the built-in tools. When reads get realigned, the MD field becomes obsolete. We have no interest in recomputing it since the MD is meant to enable variant calling without looking at the reference, which we consider a bad idea. That said, you are welcome to write an annotation module for VariantAnnotator to achieve this.
Geraldine Van der Auwera, PhD