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.
Following a short hiatus on the sample un-improvement job which may or may not have been halted by vr-pipe inadvertently knocking over a storage node at the Sanger Institute, our 837 non-33 jobs burst back in to life only to fall at the final hurdle of the first pipeline of the vr-pipe workflow. Despite my […]