I ran following command using bowtie2 version 2.1.0.
bowtie2 --mm --threads 12 -q --phred33 --very-sensitive -N 1 -L 15 -i L,0,0.1 --end-to-end -k 20 -x ref.fa in.fq -S out.sam
I noticed that in the PG flag of the sam headers, it no longer writes the command line parameters as it is done with bowtie1.
i.e. CL tag value pair is missing.
Is it a bug or am I not using the program correctly?
Any help is greatly appreciated.