First time posting here (or really forums in general), so apologies if I am breaking any etiquette.
My question regards using the mpileup feature in Samtools. I am curious if it matters whether or not it matters if I run mpileup individually for each bam file versus running mpileup as one process for all the bam files. E.g., if I have 3 bam files, 1.bam, 2.bam, and 3.bam, I can either run samtools mpileup 1.bam and then samtools mpileup 2.bam, etc or run samptools mpileup 1.bam, 2.bam, 3.bam (I know the syntax here is wrong, just trying to illustrate the problem).
The reason I'm asking: We are trying to use cluster computer resources (i.e., Westgrid), and as far as we can tell, there is no easy way to run the mpileup over multiple processors. It therefore seems like it we would be able to save a lot of time by running the mpileup individually as separate jobs on the cluster. Is this legit/would the results we get be legitimate? (It seems that read depth would decrease in the individual case?) Also, is there a convenient way to combine the resulting bcf files into a single bcf file?
Our group is very new to cluster computing and also fairly new to the whole GBS/NGS sequencing process, any help or resources you can point us to would be greatly appreciated!