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keeping read group information from a BAM file after remapping?
I'm trying to run GATK starting from a bam file with multiple read groups. I convert the bam file to interleveled fastq and realign it using BWA MEM. However neither BWA nor Picard to my knowledge allow me to reassign multiple readgroups. Would I be right to first split the original bam file by read groups, carry out alignment of the split bam files, convert them to fastq and then merge then with samtools merge so that all the read group information from the original bam file is captured in the realigned bam file?
I will be grateful for your comments and alternative methods and advice.