I have a question regarding merging the BAM files. I have several libraries 4 lanes each. I demultiplexed, mapped against the reference genome, gave the read group name, merged libraries using samtools merge and removed the duplicate reads. Now that I did variant calling I realised I have a call for 4 libraries separately, that is because I did read group name before merging. Is this the right approach? Or should I merge the libraries before doing the read group name? Generally, when is it better to do the merging step?
Bob_1_CL1.bam Bob_2_CL1.bam Bob_3_CL1.bam Bob_4_CL1.bam John_1_CL40.bam John_2_CL40.bam John_3_CL40.bam John_4_CL40.bam