Hello all,
This is an announcement intended for users of the Picard tools, which
historically have been supported through this mailing list.
As you may know, both toolkits are developed at the Broad Institute, and
are deployed together in the Broad's analysis pipelines. The fact that they
have been developed, released and supported separately so far is more an
accident of history and internal organization than anything else (and we
know it's inconvenient to y'all).
The good news is that we're taking steps to consolidate these efforts,
which we believe will benefit everyone. In that spirit, we (the GATK dev
team) have been working closely with the Picard tools development team, and
we're now ready to take the first step of consolidating support for the
tools. From now on, you will be able to ask us questions about the Picard
tools, and report bugs, in the GATK forum at
http://gatkforums.broadinstitute.org/categories/ask-the-team. And
developers will be happy to hear that we are also committed to supporting
HTSJDK for developers through the Github repo’s Issues tracker.
In the near future, we will also start hosting downloads and documentation
for the Picard tools on the GATK website. And before you ask, yes, the
Picard tools will continue to be completely open-source and available to
all free of charge.
To recap, we have brought the GATK and Picard teams together, and we are
working on bringing together in the same place all the methods and tools to
perform genome analysis. Our goal is to make a world where you can run our
complete Best Practices pipeline end-to-end with a single Broad toolkit. We
think it’ll make your life easier, because it sure is making ours easier.
Comments and questions are welcome in the GATK forum or on the GATK blog at
https://www.broadinstitute.org/gatk/blog?id=5297.
Best,
Geraldine
--
Geraldine A. Van der Auwera, Ph.D.
Bioinformatics Scientist II
GATK Support & Outreach
Broad Institute
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