Hey all :]
I use samtools's depth, and occasionally samtool's pileup commands to calculate coverage of my reads to the genome before binning for coverage. I'm pretty sure everyone else does too ;)
One very common problem is that people find "samtools depth" and "samtools mpileup" don't match up - and it's commonly attributed to filtering poor quality reads, duplicates, etc (mpileup doing more filtering).
But there's a ton of other questions I just can't get the answers too from the sametools docs, namely:
Does depth/pileup count the region between a paired reads, or just the reads themselves?
Does samtools depth/pileup count singletons in paired end sequencing? Does it extrapolate based on average read length to fillout the whole fragment?
If a read maps to multiple locations, is it counted multiple times?
I'm working with ChIP-Seq data, so i might have to correct for peak-shift. What do you guys think?