Kyle Hernandez - 2014-06-03

I am interested in trying to run virmid in separate jobs for each chromosome. I already run virmid using -af to estimate alpha on the entire BAM file, but if I wanted to split the bam files by contigs and run virmid it doesn't seem possible? It seems like Virmid would really just try to estimate alpha based on each split bam file (and probably be a bad estimate due to the random sampling). Is there a way to "trick" Virmid into thinking my split BAM files are indeed the full bam file and use the realigned/report file from it? Or, would you consider this as a bad practice?

Thanks!

Kyle