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I use --sample_name option to restrict output reads for PintReads walker (GATK version - 2.4.9).
This option works well but the output BAM header @RG still contains sample name (SM) that was not included.
Is there a way to apply this --sample_name option to BAM header at the same time?
I could reheader the BAM files using samtools but I'm looking for a better and easier way.