manta-1.3.2

Summary

This is a bugfix update from v1.3.1.

Changelog

Changed

• Move remote read retrieval for insertions to a configuration file option (MANTA-1351)
  • This feature was previously hard-coded in the workflow, the default behavior (off for cancer workflows, otherwise on) has not changed.
• Turn off the complexity filter for SV breakend graph loci containing more than two nodes (MANTA-1346)
  • High complexity elements of the SV breakend graph associated with centromeres have always been filtered out to control runtime. With this change the filtration has been slightly relaxed to ensure that true variants will not be filtered out by transitive association with a high complexity graph node.
• Turn on automated task resubmission for all workflow run modes (MANTA-1354)
  • Failed tasks have always been automatically resubmitted in SGE mode, this is now extended to localhost mode as well.
  • This change is intended to work around sporadic I/O issues on network filesystems.

Fixed

• Standardize germline FORMAT/GQ VCF tag to Integer type (MANTA-1349)
• Update to pyflow v1.1.20 to close infrequent race condition in task resolution (STREL-853)
  • Under the race condition error, a non-failing task would be logged as failing with the message "TASKNAME has stopped without a traceable cause"

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manta-1.3.2.centos6_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 6 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.3.2.release_src.tar.bz2 download is the full source code release. The “Source code” downloads are generated by GitHub and are incomplete as they are missing version numbers and build system changes to improve portability.