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Any function to add originial qualities to a BQSR bam?
My institution had a practice of routinely keeping both original and BQSR bam (output from ApplyBQSR). We are in process of shifting practice to keep both original qualities (OQ) and BQSR qualities into a single bam (using the --emit-original-quals). However, we have a large number of historical bams where OQ and BQSR qualities are in separate BAM file.
I wanted to check if there is GATK function that can to facilitate this addition of OQ to an existing BQSR bam?
Thanks.