As i'm a really biginner i'm not really sure of which tools are mandatory. I try to follow the gatk best practices for germline snp. I have human wgs data.
I done qc and trimming with fastp. Then alignment with bwa mem, then MarkduplicatesSpark.
I'm note sûre if i go on bqsr or if i need to do SetNmMdAndUqTags before ? I never see this tools in the image of best practices of gatk but in the description Web page of the tool MarkduplicatesSpark it's written
MarkDuplicatesSpark processing can replace both the MarkDuplicates and SortSam steps of the Best Practices single sample pipeline. After flagging duplicate sets, the tool automatically coordinate-sorts the records. It is still necessary to subsequently run SetNmMdAndUqTags before running BQSR.
Someone could help me please ?