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Mutect2 Sample name

AsJAsJ JPMember


I would like to use mutect2 to call variants from WGS data, I understand that GATK accept bam files that ONLY have readgroup information.
Picard tools AddOrReplaceGroups can add read group info. to the sam file.
My question is about options of AddOrReplaceGroups.jar such as sample name (RGSM), How muTect2 use this sample name information?
what about if RGSM=null for normal and disease samples? MuTect2 has already option for -I:normal and -I:tumour samples? what about RGSM sample names?

Thank you


Best Answer


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