strelka-2.9.10

v2.9.10 - 2018-11-07

This is a minor feature update from v2.9.9 which adds a method that computes de novo variant quality scores.

Added

• Add recommended de novo variant calling method and documentation (STREL-983)
  • The de novo variant quality score computation method, denovo.py, has been previously developed and maintained as a separate project. It is now added to the primary strelka distribution to make this easier for users to access.

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strelka-2.9.10.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 strelka-2.9.10.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.

strelka-2.9.9

v2.9.9 - 2018-09-13

This is a minor update from v2.9.8.

Changed

• Changed EVS threshold for RNA-seq inputs (STREL-975)
  • The EVS threshold was changed from 15 to 5 for both indels and SNVs.

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strelka-2.9.9.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 strelka-2.9.9.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.

strelka-2.9.8

v2.9.8 - 2018-09-06

This is a minor bugfix update from v2.9.7.

Fixed

• Fix depth filters for germline continuous frequency indel calls (STREL-978)
  • The LowDepth filter was being spuriously applied to all indels called through the continuous frequency model. This model is typically applied only to the mitochondrial chromosome to find heteroplasmic calls.
  • This filter is now fixed to work as documented for all variant types.

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strelka-2.9.8.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 strelka-2.9.8.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.

strelka-2.9.7

v2.9.7 - 2018-08-14

This is a minor bugfix update from v2.9.6.

Fixed

• Preserve softlinks in input reference fasta file paths (STREL-976)

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strelka-2.9.7.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 strelka-2.9.7.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.

strelka-2.9.6

v2.9.6 - 2018-07-17

This is a minor bugfix update from v2.9.5.

Fixed

• Fix realignment error when processing certain RNA-seq inputs (STREL-966)
  • Recent changes to read realignment/scoring introduced an edge case which fails on RNA-Seq reads from certain aligners - specifically when an insertion immediately follows an intron gap. The issue is now fixed.

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strelka-2.9.6.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 strelka-2.9.6.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.

strelka-2.9.5

v2.9.5 - 2018-06-25

This is a minor bugfix update from v2.9.4.

Fixed

• Fix germline joint sample failure case (STREL-955)
  • This fixes an uncommon issue where a multi-sample germline analysis qualifies for indel error rate estimation, but the estimator fails to converge for at least one sample. When this happens, the method is supposed to fallback to a set of default error parameters but was failing to do so. This is now fixed. The issue does not impact single-sample analysis or the somatic workflow.

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strelka-2.9.5.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 strelka-2.9.5.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.

strelka-2.9.4

v2.9.4 - 2018-06-08

This is a minor bugfix update from v2.9.3.

Fixed

• Fix rare instance where FORMAT/DP50, FORMAT/FDP50 and FORMAT/SUBDP50 are '-nan' (STREL-936)

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strelka-2.9.4.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 strelka-2.9.4.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.

strelka-2.9.3

Summary

This is a minor bugfix update from v2.9.2.

Changelog

Changed

• Add strict checks and improve error message for BED regions of size less than one (STREL-865/[#36])

Fixed

• Prevent an assertion for certain rarely encountered combinations of forced genotype alleles in the germline workflow (STREL-896)

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strelka-2.9.3.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 strelka-2.9.3.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.

strelka-2.9.2

Summary

This is a minor bugfix update from v2.9.1.

Changelog

Changed

• Turn on automated task resubmission for all workflow run modes (STREL-852)
  • 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

• 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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strelka-2.9.2.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 strelka-2.9.2.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.

strelka-2.9.1

Summary

This is a minor bugfix update from v2.9.0.

Changelog

Fixed

• Standardize header description of somatic snv and indel LowDepth filters (STREL-849)
  • This allows merging of the snv and indel vcf files.
• Fix build for gcc7+ and boost-1.64+ (STREL-824)

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strelka-2.9.1.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 strelka-2.9.1.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.