I'm struggling with finding explanations to the SAM flags presented on my sam file. to clarify, I am familiar with the picard tool in which one can find the meaning, only it is written very briefly and i don't know what it means de facto?
i.e I know flag No. 99 means in summary: read paired, read mapped in proper pair, mate reverse strand, first in pair. I don't understand what does "mate reverse strand" or "first in pair" mean? what read qualifies to this definition? what criteria checked?
Does anyone know a file that explains the flags with more details other than the picard tool and the Format Specification?