Can you please provide
a) GATK version used - GATK4
b) Exact GATK commands used
./gatk BaseRecalibrator \
-I /home/deepak/NEW_SAMPLE/SAMPLE3PICARDNEW/sample3_marked_duplicates.bam \
-R /media/deepak/EXTRA/Genomedir/hg38/hg38.fasta \
--known-sites /media/deepak/EXTRA/Genomedir/hg38/DBSNP/GCF_000001405.38 \
I am new to GATK. I am using BaseRecalibrator tool of GATK. I am getting the following error " A USER ERROR has occurred: Number of read groups must be >= 1, but is 0"
Why I am getting this error? where I am going wrong?
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