Part of the Pilon prep for polishing the PacBio Oly assembly is feeding it a bunch of Illumina data aligned to the PacBio assembly using your favorite aligner, in my case Bowtie2. I initially got a bunch of `.sam` files from Bowtie2 and wanted to convert them, so I turned to Google like any good person does these days. After looking at a bunch of different options, all answers pointed to `samtools view -sB file.sam > file.bam` as the preferred way to do this.
Thinking I knew what I was doing, I whipped up a quick slurm job script to convert everything and file up Pilon. It completed in less than 5 minutes, with a bunch of `.bam` files ~40kb in size. This was suspect, as their original `.sam` files were ~40gb.
After a reading the samtools manual, which corroborated the above conversion syntax, re-aligning some of the Illumina data files thinking I’d done something wrong there, and a whole bunch more googling, it turns out the `> file.bam` syntax is actually supposed to be `-o file.bam`.
Apparently the internet and documentation does not keep up with program changes as well as we’d like.
Roberts Lab 