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Old 06-19-2017, 07:35 PM   #3
Len Trigg
Registered Vendor
Location: New Zealand

Join Date: Jun 2011
Posts: 29

New stable releases are now available which include minor improvements and bug fixes.

The first of these is our full analysis suite, RTG Core 3.8.2. The changes in this version are listed below. Commercial users may download the update from our website at Non-commercial users can download the update from our website at or build from the updated source code on github at

We have also produced updated builds of our utilities package, RTG Tools 3.8.2, which is made freely available for non-commercial or commercial use alike. More information and download links are available from our website at or build from the updated source on github at

RTG Core 3.8.2 (2017-06-20)

This release primarily includes bugfixes and minor improvements:

* vcfeval: Records where the REF/ALT contain bases not permitted by the
VCF specification are now skipped (and reported in the log) rather
than terminating execution.

* vcfeval: (`combine` and `ga4gh` output modes only) These modes were
inserting a redundant VCF header entry containing the command line,
which has been removed.

* vcfeval: GA4GH output mode now supports loose positional matching of
variants (within +/-30bp by default, and adjustable via

* many: Prevent number formatting issues in non-English locales. The
locale is now forced to US.

* many: Some commands were not appending gzip termination blocks to VCF
outputs, which could result in subsequent warning messages being
produced by some third party tools.

* many: Improve the consistency of exception handling in cases where the
exception is thrown in a worker thread.

* many: Attempting to supply file lists via shell process redirection
would fail in non-obvious ways. File lists from process redirection
are not currently supported and are now checked for up-front.

* minor: When setting up rtg bash tab completion, issue a warning if an
incompatible completion function has already been installed. (This can
happen on some linux distros if you have the system `bash-completion`
package installed and attempt to tab-complete rtg before installing
rtg bash completion.)

* minor: Fix a typo in the example configuration settings in rtg.cfg
(specifically, RTG_JAVA_OPTS was incorrectly listed as
Len Trigg, Ph.D.
Real Time Genomics
Len Trigg is offline   Reply With Quote