Duplicate definition error with GATK PrintReads and MalformedReadFilter
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`.
Grokking GATK: Common Pitfalls with the Genome Analysis Tool Kit (and Picard)
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.
The Tolls of Bridge Building: Part IV, Mysterious Malformations
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 […]