manta-0.29.2

This is a minor bug-fix update from v0.29.1. Changelog:

• MANTA-277 fix rare stability issue with invalid genome region requested during insert size estimation.
• Update to pyflow 1.1.12 to improve SGE file system delay handling and fix issue between SGE and recent bash shellshock fix.

---

manta-0.29.2.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-0.29.2.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-0.29.1

This rolls up several low-impact issue fixes, in addition to ongoing RNA work:

• [#22] Add new manta developer guide to source docs
• [#21] improve fragment size estimation for very short fragments
• RNA: Improve fusion detection sensitivity
• MANTA-261 Transfer stable components from Manta windows port
• MANTA-273 fix support for "csi"-style BAM indices
• MANTA-273/[#14] allow bam index filenames in single-extension (Picard) style

---

manta-0.29.1.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-0.29.1.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-0.29.0

This release adds support for analyzing alignments in CRAM format. Sample alignments can now be provided in either BAM or CRAM (or combinations of these).

There are also two improvements to support the 1kg hg38 reference with decoy and HLA sequences: (1) improved job handling for thousands of small reference contigs and (2) improved support for contig names containing colons.

Full Changelog:

• [#12]/MANTA-267 Support contig names with colons (for HLA contigs in 1kg hg38)
• MANTA-252 Complete support for CRAM input
• MANTA-264 Remove samtools from manta dependencies
• MANTA-252 Change default chrom depth to median estimate from alignments
• MANTA-263 Improve performance/stability for references with
  large numbers of small contigs
• MANTA-261 Transfer stable components from Manta windows port

Prior WGS users note that the default method used to estimate chromosome sequence depth for the purpose of filtering high depth regions has changed to support CRAM: Manta now uses a median depth estimate from sampling chromosome regions instead of read counts from the BAM's index file. The new estimate is more robust, but may result in minor filtration differences compared to previous Manta versions.

Thanks to @jkbonfield for a key htslib edit (samtools/samtools#455) which enabled CRAM support to move forward, and @chapmanb for describing/patching the HLA contig name issue.

---

manta-0.29.0.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-0.29.0.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-0.28.0

Summary

This is a major update introducing joint analysis of multiple diploid individuals.

When provided with multiple input BAM files, Manta now builds a joint candidate SV and indel set over all samples, then analyzes supporting evidence to provide genotypes for each individual, outputting all results in a multi-sample VCF. The diploid analysis VCF output now includes PL values and per-sample filtration, and should be appropriate for post-processing to provide de-novo variant call candidates. Note that the initial target for multi-sample support is on the family scale, so behavior and stability of the method for joint analysis of more than about 10 samples is unknown. Previous manta users should consult update risks enumerated further below.

Changelog since v0.27.2:

• MANTA-259 Support joint analysis of multiple diploid samples
• MANTA-260 Add per-sample filtration to separate QUAL and GQ filters for
  diploid case
• MANTA-252 Add fast chrom median depth estimator (partally enables CRAM)
• MANTA-258 Add PL values to diploid output

Update risks

This update brings a number of minor sample processing changes which are potentially disruptive for users of older versions:

• Previously multiple BAM files were accepted for each sample and merged as a single sample (for either the normal or tumor sample). This 'merging workflow' is no longer an option.
• Sample names printed in the VCF output are now parsed from the header of each input BAM file. The name is parsed from the first @RG record found which contains a sample name, and processed to replace spaces with underscores. This replaces the previous use of "SAMPLE" for germline and tumor-only analysis and the use of "NORMAL" and "TUMOR" for tumor/normal subtraction.
• The diploid VCF output now uses SAMPLE-level filtration (the FT field from the VCF 4.1 spec). There is a new record-level filter on QUAL < 20 (called "MinQUAL"), and the previous "MinGQ" filter is now a sample filter. All other manta record-level filters are still applied at the whole-record level. Note that to simplify the transition for users who are only interested in single individual analysis, any sample filter which is applied to all samples in the VCF is copied to the record level as well.

---

manta-0.28.0.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-0.28.0.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-0.27.2

This is a minor bugfix release to provide the MANTA-257 fix. MANTA-257 is an infrequent stability problem which could impact any type of Manta analysis (germline,tumor/normal,tumor-only). It is very rare in general, but is more likely to occur when using very high numbers (1000+) of contigs, such as hg38 with all new decoy sequences or a large set of contigs from a draft genome assembly. This update also includes important RNA-Seq analysis fixes.

Full ChangeLog since v0.27.1:

• MANTA-257 Fix rare failure condition for graph merge
• MANTA-255 include zlib in build, simplify win64 development
• MANTA-254 Fix handling of off-edge splicing in the RNA Jump Intron Aligner
• MANTA-253 improve alignment corner cases and debugging features

---

manta-0.27.2.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-0.27.2.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-0.27.1

This release includes an important stability fix [#6]. This fix closes a bug which can deterministically fail certain builds based on the structure of manta's region association graph. It should be somewhat more likely to cause problems in highly rearranged genomes. Thanks to @lawrencebower for identifying and providing examples to reproduce this.

Changelog:

• [#6] Fix assertion caused by filtered graph edges on bin boundaries.
• [#5] Improve robustness to filesystem delay (update ot pyflow v1.1.7)

---

manta-0.27.1.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-0.27.1.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-0.27.0

This is a new feature release debuting @x-chen's initial implementation of tumor-only analysis.

Changelog:

• MANTA-188 fix off-by-one position issues in duplication
  and inversion VCF records
  • For duplication VCF records: POS is one less, and END is one more, than previous manta versions
  • For inversion VCF records with breakends opening to the right (with 'INV3' tag): END is one more than previous manta versions
  • For inversion VCF records with breakends opening to the left (with 'INV5' tag): POS is one less than previous manta versions
• MANTA-229 Add initial support for tumor-only analysis

---

manta-0.27.0.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-0.27.0.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-0.26.5

• Update pyflow to v1.1.6: fixes multithread bug introduced in pyflow v1.1.5. Manta should be isolated from this issue (and shows no test failures) -- issuing bug-fix update just to be sure.

---

manta-0.26.5.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-0.26.5.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-0.26.4

• Update license to GPLv3
• Update to re-licensed pyflow v1.1.5
• MANTA-244 Handle unstranded RNA data
• MANTA-239 Use RNA bam alignments for ref read scoring
• Fix core/memory auto-detect for OSX

---

manta-0.26.4.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-0.26.4.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-0.26.3

Minor build and documentation update:

• Fix OSX build and demo run (req. update to boost 1.56)
• Update travis CI OSX build, static analyzer

---

manta-0.26.3.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-0.26.3.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.