GATK indel realignment: recomputing the MD field
Posted in Ask the GATK team | Last updated on


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Hi,

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?


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