I would like to compute the contig coverage I got from an assembly.
I have different lib (of insert size) so i've mapped it separately, at the end I have a .bam file for each library:
Now I would like to give it to BBmap pileup.sh for coverage computation.
But I think I have to merge the 2.bam files with :
samtools merge output.bam *.bam
I'm not sure, Is it the right way to do ?