I am not a very organised bioinformatician, and despite your best efforts, you probably aren’t either. I’ve written a tool called `chitin` that tries to keep me, and bioinformatics more organised.
I wanted a BAM that contained reads aligned to just one of the many contigs the file contained. As usual, I made this much more difficult than it really ought to have been.
Recently I’ve been following the GATK DNASeq Best Practice Pipeline for my limpet sequence data. Here are some of the mistakes I made and how I made them go away.