So, I'm through the process of learning how to perform variant calling and doing some reading/tutorials, etc. I'm using the "BWA-MEM -> Samtools mpileup" strategy to do so.
I figured that some people use bwa-mem with the -R option, which will add read group information to samples. But I did not get how useful that is in my case because some people also don't apply the -R option. Basically I´m analyzing plant organisms WGS data. The samples are all siblings derived from a crossing. It`s paired end data and my sample nomenclature follows the pattern:
So, I arleady generated a VCF file containing all the identified SNPs. I ran BWA-MEM without the -R option. No warning was generated nor mpileup complained about anything. So, it's best for me to use the -R option or that wouldn't change much?
Thanks for the help.