I was bemused to find a Linux live disk unable to identify the storage volume on my new Dell XPS 13 laptop. It seemed I needed to change the SATA controller mode from `RAID` to `AHCI`, but Windows had other ideas. Unable to find a solution online that didn’t cause a boot BSOD, I found my own.
This afternoon I wanted to quickly check whether some reads in a BAM would be filtered out by the GATK `MalformedReadFilter`. Turns out that GATK is pretty unforgiving if you forget that filter is automatically applied by `PrintReads`.
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.