i am using the samtools pileup tool to get the per base coverage, and it seems to be working great. the problem is that i seem to get different read coverage when i perform the pileup on the original bwa sam file (that includes unmapped and non uniquely mapped reads) and when i perform the pileup on the same sam file only filtered for uniquely mapped reads.
the coverage is slightly higher when i use the unfiltered sam file, but if it includes non relevant reads, maybe i should stick to the uniquely mapped reads.
your opinion? thanks.