This might be a bit duplicate question, but previous posts did not help me.
I have a reference sequence, I map reads on it and get .bam file. Now I would like to get number of reads overlapping every single base in my reference sequence (=coverage per base).
Secondly, I would like to get the number of bases at these positions, like:
pos A C G T 1 A:2 C:3 G:0 T:1 2 A:2 C:3 G:0 T:1 3 A:0 C:0 G:0 T:7 4 .. ..
Thanks a lot!