Sadly Broad Institute's great contribution to new generation sequencing NGS, GATK, is not open source anymore.
GATK 2.0 is moving to a mixed open/closed-source modelPersonally I dislike this movement. If reason is money there are successful business models build around open source software without the need of leaving the open source community.
The complete GATK 2.0 suite will be distributed as a binary only, without source code for the newest tools. We plan to release the source code for these tools, but its unclear the timeframe for this.
Doing this sort of things is a sacrilege for many of the members of our community fighting day and night for the #OA. I can see RMS deeply depress and crying in a corner every time such a thing happens. Whatever the reason behind this change is, presumably it has been a long meditated one. So I would expect a better explanation of why this change was needed, why keep being an open source software was impeding this goal, and what is more important, the thing that annoys me more, and denotes poor strategic plan for such a big change "We plan to release the source code for these tools, but its unclear the timeframe for this". Hummm, this seems to me that commitment for open source has vanished here. Even if you believe in OS, some times you are forced to make concessions to close software but I would expect to leave clear note when and how your source code would be open again.
How come we are going to lead a war for open access journals and against patents but want to make money of our software. This seems a deadly friendly fire to me until I read a good detailed explanation of the reasons behind.
It is a good thing to have samtools around as a backup.
== follow up ==