manta-v1.6.0

v1.6.0 - 2019-06-25

This is a significant engineering update from the v1.5.1 release, in which the SV candidate generation step has been changed to a single multi-threaded process to improve task scheduling. This slightly improves average runtime and reduces runtime variability. With this update, support for job distribution over SGE is dropped.

Added

• Add configuration option to turn off the evidence signal filter during candidate generation (DRAGEN-1873)
  • This enables very high sensitivity during high depth tumor-only calling

Changed

• Change the SV candidate discovery and genotyping phase from a multi-process to a multi-thread design for better CPU utilization (MANTA-1521)
  • As a result, runtime is faster and less variable than before.
  • Runtime improvements vary by workload and server configuration, for typical WGS workloads on a modern server an improvement of ~5-10% may be expected, but improvements of up to 50% have been observed for cases where work previously was poorly distributed across processes.
  • SGE support is removed with this change.
• Update htslib/samtools to 1.9 (MANTA-1483)

---

manta-1.6.0.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-1.6.0.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-1.5.1

v1.5.1 - 2019-02-15

This is a minor update from v1.5.0.

Fixed

• Fix a bug in selecting large insertion candidates (MANTA-1496)
• Fix a minor bug in small SV alignment QC (MANTA-1498)

---

manta-1.5.1.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 manta-1.5.1.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-v1.5.0

v1.5.0 - 2018-11-12

This is a major update from v1.4.0, featuring improved precision and stability, a new configurable option of overlapping pair reads, and a few bug fixes. VCF representation is improved by introducing a couple of new filters and representing inversions as two breakend records.

Please note the changed format of inversions in the output VCF files. A supplementary script is provided that can be applied to Manta's output VCF files to reformat inversions into single inverted sequence junctions, which was the format used in earlier versions than this release. The details are described in the section "Inversions" of the Developer Guide.
https://github.com/Illumina/manta/tree/master/docs/userGuide#inversions

Added

• Add a configurable option to allow overlapping pairs to be used as evidence (MANTA-1398)
  • The option is available in the configure file configureManta.py.ini

Changed

• Change SV candidate contig aligners to improve precision (MANTA-1396)
  • Change contig aligners such that variant occurrences are more heavily penalized.
• Fix multi-junction nomination (MANTA-1430)
  • Complex events with more than two junctions are no longer nominated as a group
  • Fix the problem of duplicate detection of the same SV candidate
• Add index to ensure uniqueness of evidence bam filenames (MANTA-1431)
  • It solves the potential problem of name conflicts for evidence bams if the input bam files have the same name while located in different directories.
• Change filters for easy interpretation of multi-sample germline variant vcf (MANTA-1343)
  • Add record-level filter 'SampleFT' when no sample passes all sample level filters
  • Add sample-level filter 'HomRef' for homogyzous reference calls
  • No more sample-level filter will be applied at the record level even if it applies to all samples
• Change representation of inversions in the VCF output (MANTA-1385)
  • Intrachromosomal translocations with inverted breakpoints are now reported as two breakend (BND) records.
  • Previously they were reported in the VCF using the inversion (INV) allele type.

Fixed

• Fix the bug of stats generation with short reference sequences (MANTA-1459/[#143])
• Fix the evidence significance test in the multi-sample calling mode (MANTA-1294)
  • This issue previously caused spurious false negatives during the multi-sample calling mode. The incidence rate of the problem tended to increase with sample count.

---

manta-1.5.0.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-1.5.0.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-1.4.0

v1.4.0 - 2018-04-25

This is a major bugfix update from v1.3.2, featuring improved precision and vcf representation, in addition to minor user friendly improvements.

Changed

• Refine SV candidate filter to improve precision (MANTA-1310)
  • Change assessment of assembled SV candidate contigs such that indel occurrences near breakends are more heavily penalized and indel extension penalties are removed.
• Improve the accuracy of SV breakend position for precise calls (MANTA-1178)
  • Expand the reference sequence for the rare cases where a detected breakend is close to the reference end.
• Improve sensitivity for RNA calling (MANTA-1330)
  • Reduce the length of reference sequence to which an assembled SV candidate contig is aligned.
• Add strict checks and improve error message for BED regions of size less than one (STREL-865)
• Improve user guide to clarify meaning of the INV3/INV5 vcf INFO tags (MANTA-1305)
• Remove BND from vcf ALT field to comply with vcf spec (MANTA-1314)

Fixed

• Fix the off-by-1 bug for vcf HOMSEQ tag in certain variant types (MANTA-1311)
  • Due to position adjustment for certain breakends of inversions and duplications, HOMSEQ was off-by-1 for those variants.
• Fix a bug in breakend homology logic for large variants (MANTA-1313)
  • The breakend insertion was not considered previously when identifying breakend homology sequence.

---

manta-1.4.0.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-1.4.0.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-1.3.2

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"

---

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.

manta-1.3.1

Summary

This is a bugfix update from v1.3.0, notably providing an htslib update to address issues with running manta from alignments in CRAM format.

Changelog

Changed

• Change default minimum scored SV size from 51 to 50 (MANTA-1321)
  • This change is intended to better align with GIAB SV size range conventions.

Fixed

• Update htslib to incorporate CRAM file query fix (MANTA-1336/[#109])
  • This is expected to resolve all known issues with manta from alignments in CRAM format.
• Fix RNA-seq split read count regression introduced by MANTA-1332 in the v1.3.0 release (MANTA-1342)
• Stop forcing static linking for zlib (STREL-842)
  • This change brings zlib policy in-line with strelka, such that options (i.e. LD_PRELOAD) are available for improved compression performance.

---

manta-1.3.1.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 manta-1.3.1.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-1.3.0

This is a major update from v1.2.2. It features improvements to candidate SV precision and genotyping accuracy, in addition to minor improvements in stability, runtime and error diagnostics.

Changed

• Change depth estimation read filter to better match the filter used for variant calling (MANTA-1296)
  • Expected depth per chromosome and local depth per locus/variant are now computed after removing filtered, pcr-duplicate, and secondary reads.
• Lower default memory requirements for scatter phase tasks (MANTA-1307)
  • Reduce from 2Gb to 1.5Gb to enable all cores by default on AWS c4.8xlarge/other c* servers.
  • Added new --callMemMb option to override this value for cases of extreme depth/chimera rate, etc
• Update htslib/samtools to 1.6 (MANTA-1331)
  • Updated from older 1.2 version to include improved checks on corrupted data.
  • Stopped vendoring zlib as part of this update, so zlib (w/ headers) is now a build requirement.
• Update the genotyping model (MANTA-1205)
  • Allow minor evidence of reference allele for hom-alt calls to tolerate a small number of noisy reads.
  • Filter out split reads with poor alignments to both alleles.
• Change the eligibility filter of split reads to only consider the most likely allele (MANTA-1332)
  • A split read is allowed to contribute to the split-read evidence if its alignment to the most like allele passes the eligibility filter.

Fixed

• Provide clear error message when attempting to configure/run with python3 (MANTA-1285)
• Improve error message/docs for alignment records with unknown sequence (SEQ='*') (MANTA-1295/[#111])
• Improve error message when two alignments use the same QNAME/read-number (MANTA-1293)
  • Message changed to help end-users track down the issue in the alignment file more easily - now includes chromosome name instead of contig index and 1-indexed alignment position.
• Fix CRC error from python gzip lib when generating evidence bam (MANTA-1270)
  • Remove the filter on evidence reads for SV candidates that are not in the file candidateSV.vcf.gz, because the file now contains all SV candidates without removing duplicates.
• Stop automatically clearing python environment variables (MANTA-1316)
  • This should allow python from certain module systems to be used, but may (rarely) cause instability due to conflicting content in a user's PYTHONPATH.
• Improve estimation of chimeric fragment rate (ie. fraction of reads which are split or in anomalous pairs) (MANTA-1261/[#103])
  • This fraction is used to set signal/noise thresholds important for somatic calling.
  • The secondary/supplemental segments of each split read are no longer counted as separate observations.
  • The method now accounts for many reads being classified as both anomalous and split.

---

manta-1.3.0.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-1.3.0.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-1.2.2

This is a minor update from v1.2.1

Added

• Add a configurable option graphNodeMaxEdgeCount (MANTA-1247)
  • During SV candidate generation, if both nodes of an edge have an edge count higher than the configured value, that edge will be skipped for evaluation.

Changed

• Test for unsupported BAM SEQ format (MANTA-1265)
  • Test the input bam reads for use of the = symbol in the SEQ field, and provide a clear error message if this is found.
• Verify run directory has not already been configured (MANTA-1252/STREL-734/[#102])
• Update minumum boost version to 1.58 (MANTA-1250)
• Update minimum supported linux OS from Centos 5 to 6 (MANTA-1249)

Fixed

• Fix imprecise SV filtering when CIEND is a subset of CIPOS (MANTA-1146)
• Ensure consistent BND pairs for translocations or RNA fusions are selected during vcf merging (MANTA-1243)
• Fix manta to tolerate deserialization differences in boost above/below v1.58 (MANTA-1262)
  • Impact of issue was an (infrequent) assertion using boost v1.58+: Assertion 'size() == rhs.size()' failed
  • Change in boost policy for certain vectors causes vector append in some instances that were previously overwritten.
• Fix target region retrieval (MANTA-1264)
  • The bug was in retrieving overlapping subregions specified by "--callRegion" and "--region" when the argument of "--region" has chromosome name only.

---

manta-1.2.2.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-1.2.2.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-1.2.1

This is a minor update release:

Added

• Use the BAM mate CIGAR (MC) tag, when present, to improve the accuracy of accessing if a read has extended into adapter sequence (MANTA-1097)
• Add sanity check of specified target regions during configuration (MANTA-1218)
  • A configuration error, instead of a runtime error, will be generated if the chromosome portion of the region does not match a chromosome name from the input reference sequence.

Changed

• Change candidateSV.vcf to include all candidates used to generate final calls (MANTA-1039)
  • The candidates may include redundanta entries.
  • Redundant candidates are still reduced to a single best call in the final call output.
• Move changelog to markdown format (MANTA-1245)

Fixed

• Fix an issue in the contig output feature introduced in v1.2.0/MANTA-1207, such that contigs are provided for all SV types (MANTA-1236)

---

manta-1.2.1.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 manta-1.2.1.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-1.2.0

This is a major feature update from v1.1.1. The release includes

• The improved iterative assembler being the default assembler
• Several improvements in calling RNA-seq data
• A couple of new features including contig output for DNA data and specification of an existing alignment stats file
• A few improvements in providing more specific messages to users
• A number of bug fixes

Full ChangeLog:

Added

• MANTA-696 Improve the iterative assembler and set it to the default assembler
• MANTA-1207 Add an optional feature to output contig in vcf
• MANTA-1215 Add an option for specification of an existing alignment stats file
• MANTA-1043 Add more read statistics when 'too few read pair observations' exception
• MANTA-886 Add verification of the extension of alignment input file
• MANTA-1118 Add QC check of read length
• MANTA-1044 Enable build on more architectures
• MANTA-1231 Enable clang5.0 build

Changed

• MANTA-445 RNA: Select contigs for refinement based on alignment score and read count
• MANTA-443 Improve the check of running into adapter for data with small insert size
• MANTA-1177 Improve CRAM reference handling
• MANTA-1041 Improve exception message context to include associated read and SV candidate info
• MANTA-1116 Sort duplicate vcf entries together to allow merging

Fixed

• MANTA-1211/[#99] Fix issue with empty regions input to EstimateSVLoci
• MANTA-1038 Fix infrequent graph edge lookup failure
• MANTA-1175 Fix a bug of duplicate RG & PG in evidence bams
• MANTA-865 Fix sortVcf.py to handle vcf files without a header

Please note that starting from this release, the linux binary distribution is built on CentOS 6.

---

manta-1.2.0.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-1.2.0.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.