Can't add read group correctly to minimap2 sam alignmnet
Hello
I am running minimap2 in a pipeline with GATK that needs read group data @RG with sample information.
minimap2 -ax sr -t 20 -I 100G -R @RG\\tID:A00253_251_HTN2JDSXY.2\\tPL:ILLUMINA\tLB:LB1\\tSM:TA90 ref.mmi reads_1.fq.gz reads_2.fq.gz | samtools view -bh -F 260 -T ref.fa >out.bam
I see in the bam file only the ID part of the read group like this:
RG:Z:A00253_251_HTN2JDSXY.2
How do I fix this? Thank you
1 answer
Eventually I got an answer from the developer of minimap2 saying that I did it correctly and the output in the bam file is in the format is should be. The sample information is given only in the bam/sam header and not in each read. I used the bam file in GATK and there was no problem.
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