manta-1.1.1

The release introduces a new feature to allow specification of call regions in a bed file. The details are described in the section "Call regions"of the User Guide.
https://github.com/Illumina/manta/blob/develop/docs/userGuide/README.md#call-regions

The release also includes several improvements in calling RNA-seq data and a couple of bug fixes.

Full ChangeLog:

• MANTA-691 Add an option to specify call regions in a bed file
• MANTA-977/[#83] Improve SA tag error reporting
• Manta-894 Add INTRON_OPEN penality to off_edge splicing
• Manta-586 Add RNA filters to vcf
• MANTA-962/[#79] Add a user error for missing ini file
• MANTA-554 Disable multiJunction scoring logic in RNA mode
• MANTA-625 Add RNA-mode specific rnaMinCandidateSize option
  • With default set to disable small variant calling
• MANTA-449 Move RNA-mode output to RnaSV.vcf.gz;
  • Remove GT and related fields and filters
  • No longer output unpaired breakends

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manta-1.1.1.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.1.1.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.

manta-1.1.0

This release includes the following feature enhancements and bug fixes:

• Improved the robustness of the stats generation module estimating fragment size distribution.
• Fixed the problem of inaccurate genotyping multi-junction events with multiply samples.
• Fixed the bug of ill-formatted DELs due to unknown size insertion component.
• Merged the previous RNA specific branch and updated the RNA mode configuration.
• There are also documentation, source format and library/build changes.

Full ChangeLog:

• Manta-677 Stats generation
  • Add a sampling buffer to skip regions with a large number of abnormal reads
  • Add a compiler flag to output fragment-size cdf in stats summary
• Sync shared library/build changes with strelka
• Scratch: Merge src formatting changes from strelka
• Docs: Update comments in automated TOC generation; Fix nonstandard markdown links
• MANTA-583 Document multi-junction handling
• MANTA-518 Add sample level check of genotyping for multi-junction events
• MANTA-486/[#57] clarify rna mode configuration/improve errors
• MANTA-436 Classify indels with unknown size insertions as insertions
• MANTA-304 Merge RNAMaster branch
  • RNA: Include some spliced reads in insert-size estimation
  • RNA: Include split-reads as evidence for imprecise translocations
  • RNA: Use proper-pair BAM flag for abnormal pair detection

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manta-1.1.0.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.1.0.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.

manta-1.0.3

This is a minor update including a couple of bug fixes.

Full Changelog:

• MANTA-302 fix the bug of duplicate variant ID
• MANTA-279 fix the bug of reporting variants beyond chromosome end position

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manta-1.0.3.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.0.3.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.

manta-1.0.2

This release is a minor update that fix the denovo scoring script to write valid vcf when the input vcf contains more than three samples.

Full Changelog:

• Update denovo scoring script to write valid vcf when the input vcf contains more than three samples
• Remove old/unused reference utility functions

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manta-1.0.2.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.0.2.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.

manta-1.0.1

The release introduces a new feature to invoke manta's assembler on a specified set of input reads. This feature was developed for debugging purposes, and the details are described in the section “Test assembler directly from BAM input” of the Developer Guide.
https://github.com/Illumina/manta/blob/master/docs/developerGuide/testAssembler.md

The release also includes cleanups for handling split read evidence with a couple of bug fixes.

Full Changelog:

• MANTA-299 documentation and method cleanup for handling split read evidence with a couple of bug fixes
• MANTA-296 Test assembler directly from bam input
• [#43] fix freed string pointer use in sample name

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manta-1.0.1.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.0.1.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.

manta-1.0.0

This release is a stable upgrade of v0.29.6, with the same SV calling methodology and consistent performance. The release introduces a new feature to generate bam files of evidence reads for SVs listed in the candidate vcf file. This feature was developed for debugging purposes, and the details are described in the section “Generating evidence bams” of the User Guide.
https://github.com/Illumina/manta/tree/master/docs/userGuide#generating-evidence-bams

Full Changelog:

• MANTA-290 add a debugging option to generate candidate SV evidence BAMs
• [#36] support setting SGE task runtime limit
• Format change of de novo calls, moving DQ from INFO to FORMAT
• [#40] improve robustness to user locale settings
• close infrequent memory leak in hts_streamer
• A number of changes in build and docs

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manta-1.0.0.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-1.0.0.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.

manta-0.29.6

This release fixes a bug in the default assembler of manta that may lead to failure of assembly or incorreclty assembled contigs.

Full Changelog:

• MANTA-287 fix a bug in the small assembler by checking consistency when adding a new supporting read of contig.
• MANTA-287 add the unit test of consistency of supporting reads

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manta-0.29.6.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-0.29.6.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.

manta-0.29.5

This is a minor bugfix update, primarily motivated by [#32], wherein manta would fail when given a soft-linked bam/cram file with a non-linked index (bai/crai) file, such as by running:

ln -s /other/path/sample.bam
samtools index sample.bam
configManta.py --bam sample.bam [other args...]

Changelog:

• [#32] Preserve file path softlinks so that sidecar index files can be found
• Fix field name in denovo variant search script

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manta-0.29.5.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-0.29.5.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.

manta-0.29.4

This release adds a python script to support de novo calling in trios, based on the previous feature of joint calling of multiple diploid samples.

It also includes improvements of windows shell support and reorganization of configure & documentation.

Full Changelog:

• Add a python script to identify de novo calls (more details in User Guides)
• MANTA-285 add option to keep all temp files to support workflow debug
• MANTA-276 mv configure to top-level, mv guides to docs dir, add methods docs
• MANTA-284 improve windows shell support by shortening very long cmdlines

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manta-0.29.4.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-0.29.4.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.

manta-0.29.3

This is a bug-fix update from v0.29.2. Changelog:

• MANTA-280 filter supplementary reads without SA tags and read pairs with unmatched mate information
• STARKA-306 fix rare chunk size boundary defect in RangeMap

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manta-0.29.3.centos5_x86_64.tar.bz2 is a binary distribution for 64-bit linux. This is built on CentOS 5 with all dependencies except glibc statically linked. It is expected to run without modification on most linux distributions.

The manta-0.29.3.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.