This is a basic question so maybe someone can make the best of it and explain some basic details so that newbies can benefit from it.
I have been using samtools commands from other people that I think know what their doing.
The commands I have been giving are
view piped to
samtools view -u someones.bam chrY:2709520-57443438 | samtools mpileup -B -Q reference.fa - > outfile.txt
I tried to run the
mpileup command without view and it's just as fast.
Why would I want to pipe