I have aligned my WGS samples to a the latest bovine reference(B.tau5.0), available at NCBI. It is just yesterday, that in a pipeline used by 1000bull genome project, they have used the same reference merging the Y chromosome in it (B.taur5.0Y).
Now, I am not sure about it. Should I align all of my samples again? It would take huge time and resources. Is there any way to compensate and add the Y chromsome alignment that could save the current bams?
Any help is greatly appreciated.
I used bwa-0.7.17 and bwa mem for the alignment.