talk:scripts:alignment
In the alignment code, I suggest including the -R (read group information) parameter, as it is important for downstream variant calling. Adding it will not interfere with other steps if you are not proceeding with alignment. Here's an example of how to include it:
bwa-mem2 mem -R '@RG\tID:sample_1\tLB:sample_1\tSM:sample_1\tPL:ILLUMINA' -t 30 ref.fa sample_1.filtered.fq.gz sample_2.filtered.fq.gz
ID: Read group identifier (unique per sample or run). LB: Library identifier. SM: Sample name. PL: Sequencing platform (e.g., ILLUMINA).
talk/scripts/alignment.txt · Last modified: by 37.26.174.181