Hi Brent,

Thanks for maintaining and answering questions on bwa-meth. I am not sure I understand the YD and YC tags that are set by bwa-meth. My understanding so far:

YD tag makes note of the direction of mapping: whether it maps to the forward (f) or reverse (r) strand of the reference genome.

YC tag tells you whether or not your read mapped back to the C to T or G to A converted genome.

As bwa-meth assumes directional libraries, shouldn't the YD / YC tags always be f + CT and r + GA? When parsing through some bwa-meth aligned files, I noticed that some reads contain r + CT as well as f + GA.

Thanks for your help!