bamtools
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feature request: allow custom SM tag in the merged bam header
For some tools (e.g. Sentieon bam_to_vcf), one unique SM tag is needed in the input bam mapping. However the merged bam file can have multiple @RG lines that contains several different SM tags which can't be used as input for those tools.
It would be useful to have an option for the bamtools merge command to allow users to customize the SM tag in the output bam header so it is identical across all @RG lines. It could be free text, or it could be a choice by choosing one from several existing SM tags from the input bam files.
I understand different read groups should have different SM tag to tell samples apart. But some samples do have the same SM tags from the same sample with different RG IDs if the sequencing was run on multiple lanes.