I'm reading abput BWA for my project which involves SNP calling for whole genome pool-seq data. I've noticed a few online tutorials for BWA-MEM specify the -M option for a basic alignment. I don't understand what this option is doing.
Reading the manual it says;
-M Mark shorter split hits as secondary (for Picard compatibility).
What does 'split hits' mean?
What types of data should this option be used for?