How (not) to subset a BAM for GATK
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.
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.