Bam header RG conflict

[arnavaz]

Describe the bug

The header in the bam files that are created by bwa aligner have two instances of @rg written in the bam header and GATK tools have issues with that. Example:
@rg ID:1 SM:SE17-1161_N_cfDNA-010-R1.fastq.gz PL:Illumina
@pg ID:bwa PN:bwa VN:0.7.15-r1140 CL:/mnt/work1/software/bwa/0.7.15/bwa mem -M -t4 -R @rg ID:1 SM:SE17-1161_N_cfDNA-010-R1.fastq.gz

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