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.
- 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
--callMemMboption 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.
- 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/supplmental 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.
This is a minor update from v1.2.1
- 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.
- 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)
- 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.
- Impact of issue was an (infrequent) assertion using boost v1.58+:
- 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.
This is a minor bugfix release from v1.2.0
- 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.
- 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)
- 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)
This is a major feature update from v1.1.1
- 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
- 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
- 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
- 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
- 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
- MANTA-302 fix the bug of duplicate variant ID
- MANTA-279 fix the bug of reporting variants beyond chromosome end position
- SPW-316 update denovo scoring script to write valide vcf when the input vcf contains more than three samples
- Remove old/unused reference utility functions
- 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
- [#36] support setting SGE task runtime limit
- MANTA-290 add debug option to generate candidate SV evidence BAMs
- 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
- MANTA-287 add the unit test of consistency of supporting reads
- MANTA-287 fix a bug in the small assembler by checking consistency when adding a new supporting read of contig
- [#32] Preserve file path softlinks so that sidecar index files can be found
- Fix field name in denovo variant search script
- Add a python script to identify de novo calls
- 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
- 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
- MANTA-277 fix invalid genome region requested during insert size estimation
- Update to pyflow 1.1.12 to improve SGE filesystem delay handling and fix issue between SGE and recent bash shellshock fix
- [#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-267/[#12] 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
- 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
- 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
- [#6] Fix assertion caused by filtered graph edges on bin boundaries.
- [#5] Improve robustness to filesystem delay (update ot pyflow v1.1.7)
- MANTA-188/[#4] fix off-by-one position issues in some precise duplication and inversion breakends
- MANTA-229 Add initial support for tumor-only analysis
- Update pyflow to v1.1.6: fixes multithread bug introduced in v1.1.5.
- Manta should be isolated from this issue in theory.
- Update license to GPLv3
- Update to relicensed 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
- Fix OSX build and demo run (req. update to boost 1.56)
- Update travis CI OSX build, static analyzer
- MANTA-242 cleanup code portability and documentation:
- Updated all build/installation and contributor guidelines
- Updated Manta user guide
- Added Travis CI configuration file for clang/gcc build and demo run
- Minor code edits to clean compile on OS X 10.9, CentOS 5,6,7, Ubuntu 12.04 and 14.04
- Updated demo: new dataset covers COSMIC HCC1954 variants, added test to verify expected output from demo run.
- Remove python reflection from run configuration process, fixes rare config issue
- VCF output formatting: FileData corrected to FileDate
- MANTA-224 improve short-fragment handling for RNA
- MANTA-235 kmer reference mask to accelerate RNA contig alignments
- MANTA-232 filter large SVs with no read pair support
- MANTA-236 expand conditions for large insertion search to normalize BWA-mem/Isaac performance
- MANTA-231 expand scoring phase split read search around breakends to find soft clipped ref and alt support.
- MANTA-234 remove discovery pair counts from scored output files
- MANTA-222 support bwa-mem '-M' split read format
- MANTA-218 filter spanning candidates without significant signal/noise
- MANTA-155 handle N's and lowqual bases during assembly
- MANTA-219 Build system improvements for auditing, visual studio support
- MANTA-217 Improve runtime for large min candidate size settings, creating a high speed large-event mode.
- RNA - parameter adjustments, additional vcf output, orientation fixes
- MANTA-187 treat split reads symmetrically to improve RNA fusion detection
- detect split reads directly rather than via associated soft-clip sequence
- exclude split reads from contributing to local assembly evidence
- MANTA-213 FFPE runtime optimization:
- Recognize new BAM format for fragments shorter than read length, prevent these reads from triggering assembly.
- Improve insert size distribution estimation by including fragments shorter than read length.
- Add new runtime instrumentation report for candidate generation
- Add runtime summary to existing graph report
- Reduce SW edit matrix size with short k-mer match bounds on ref seq
- Improve graph noise filtration by testing specific region for evidence signal threshold
- Use adaptive noise rates in hypoth gen step: background read anomaly rate is used to determine if signal is significant. Currently applies to small assembly candidates only.
- Collapse redundant assembly candidates for small indels to single copy
- MANTA-206 Disable remote read search in T/N analysis
- MANTA-195 Improve filtration of short fragments in FFPE samples
- MANTA-200 Add filter for overlapping diploid calls which can't be explained as two haplotypes.
- MANTA-199 Fix low-frequency fragment/breakpoint mismatch (primarily an issue when large numbers of short ref contigs were used)
- Add CRAM support for individual tools - still need a quick chrom depth estimator for full workflow CRAM support
- c++11 update
- MANTA-185 remove transloc calls with neg position (from circular genome)
- [mantadev] #1 Fix SA split read breakpoint position
- MANTA-183 handle paired/single read mixture in input alignments
- MANTA-182 submit config on cmdline
- MANTA-181 fix assembler path and coverage issues
- MANTA-177 filter redundant partial insertions
- MANTA-142 improve contig alignment for large events
- MANTA-160 add pseudo-coloring to assembly, and improve multi-pass read/contig association
- MANTA-170 improve pair allele support accuracy
- MANTA-139 add shadow and chimera reads into pair counts
- MANTA-167 semi-mapped som pair correction
- MANTA-156 filter out assm poison reads
- MANTA-161 make assembly robust to seed k-mer selection
- MANTA-164 batch retrieve assembly mate reads
- MANTA-158 improve small indel contig alignment specificity
- MANTA-146 use MAPQ0 mate reads in assembly
- MANTA-48 use shadow reads for split scoring
- MANTA-157 improve shadow read filter
- MANTA-153 fix diploid prior
- MANTA-150 fix SV scoring size cutoff
- MANTA-148 check bam records for region errors
- RNA: rna-scoring
- Lower default min candidate size to 8
- MANTA-136 turn on conservative large insertion calling
- MANTA-126 multi-junction SV scoring
- MANTA-131 improve large somatic sv specificity with expanded supporting evidence search
- RNA: track candidate orientation
- MANTA-127 RG based insert stats (default off)
- MANTA-128 Improved pair orientation estimation and error checks
- RNA: Improve fusion specificity
- MANTA-125 add experimental large insertion calling (default off)
- MANTA-125 add tier2 permissive split score to reduce small somatic FP deletions
- MANTA-125 add tier2 chimera rate to reduce somatic FP calls
- MANTA-125 modify pair weight for small SVs
- MANTA-120 Improve stability of SV scoring as a function of read length
- Filter SA split read segments by MAPQ value
- MANTA-116 better handle BWA-mem SA split-reads for inversions
- MANTA-118 static libstdc++ for gcc 4.5+
- MANTA-117 add somatic quality score
- fix SA tag parsing
- MANTA-27 accept bam/fasta filenames with spaces
- MANTA-108 combine clip/semi-aligned evidence detection, don't detect overlapping reads as assembly evidence
- MANTA-98 make fewer bam scans during scoring
- MANTA-106 add high depth limit to candgen and assembler
- MANTA-75 Better match reads to SV candidates to improve runtime and lower repeat observations (part 2)
- MANTA-105 filter poorly supported candidates to reduce per-edge compute time
- MANTA-103 fix issue in RNA and WES modes introduced by MANTA-99
- MANTA-102 filter calls with high MQ0 fraction
- MANTA-99 add high-depth graph filter to improve FFPE runtime
- MANTA-100 allow for neighboring variants during assembly
- MANTA-83 sort vcfs in bam chrom order
- MANTA-96 Keep matching read pairs after candidate generation read buffer fills
- MANTA-89 Use semi-mapped read pairs to improve germline/somatic classification.
- MANTA-92 Add edge runtime performance log
- MANTA-75 Better match reads to SV candidates to improve runtime and lower repeat observations
- MANTA-85 Increase uniformity of tags in vcf output
- First complete pass at installation and user guide
- MANTA-81 Fix small indel somatic false negatives introduced in MANTA-63
- MANTA-80 Additional workflow options: run subsections of the genome, finer task parallelization control and merge multiple input BAMs per sample.
- MANTA-63 Incorporate read-pair evidence into small SVs/indels
- MANTA-77 Fix assertion for rna-seq test
- MANTA-17 Include semi-aligned reads in discovery and scoring
- MANTA-69 Update score/write filter to account for CIGAR and SA-read candidates, and new uniform candidate scheme for self-edges.
- MANTA-70 Correct filters to allow for small inversion and tandem dup detection
- MANTA-68 SVLEN not set correctly for non-deletions
- MANTA-64 Improve candidate generation for small regions
- MANTA-43 allow manta installation to be relocated
- MANTA-55 compile python code as part of build/install
- MANTA-58 fix issue with breakends near contig boundaries
- MANTA-61 add markdown-based user guide to build
- MANTA-30 initial integration of known variant tracing framework
- MANTA-20 incorporate split-reads into quality score
- MANTA-42 SV finder mismatches various read pair / sv-candidate combinations
- MANTA-53 Enable --rescore option in runWorkflow.py
- MANTA-40 Don't call splicing-events in RNA-seq as deletions
- MANTA-20 include split read counts for short reads
- MANTA-44 Fix Rhodobacter analysis
- Adjust all vcf output to pass vcf-validator
- MANTA-20 fix split read breakpoint location
- Fix low-frequency assertion due to unexpected alignment pattern
- MANTA-20 Limit split read counts to those uniquely supporting each allele, where P(allele|read)>0.999
- MANTA-20 Add likelihood based QUAL,GQ scores to diploid output, adjust thresholds of somatic output to incorporate ref pairs and split reads.
- MANTA-41 Fails when chrom name not in [a-zA-z0-9_-]+
- MANTA-25 Partial support for BWA-MEM SA split reads
- MANTA-36 Segfault on RNA-Seq BAM input
- MANTA-20 Combined reference spanning read and split read evidence per variant
- MANTA-20 Diploid vcf output for non-tumor sample, diploid genotype inference score still todo
- MANTA-39 prevent crash on large CIGAR deletions
- MANTA-20 split read evidence counts for all large spanning SVs
- MANTA-20 preliminary work on this branch allows assembly skip and control of min indel candidate size and min indel score size
- MANTA-33 reduce SV graph ram requirement to ~1/3 of its previous value, increase all post-merge task memory requests.
- MANTA-17 merged shadow reads into assembly and adjusted assembly parameters. Large (50+ base) insertion sensitivity improves by ~.35-.4 as a result.
- Improvements to vcf output and cmake build.
- MANTA-28 Add prototype discovery/local-assembly of small events down to 10 bases
- MANTA-24 Better handle very high depth and chimeric noise complexity based on BWA-mem FFPE examples
- MANTA-26 Extend fragment stats to provide estimate of full fragment size distribution
- Large event assembly fixes
- MANTA-23 enable use of pre-existing depth and stats files (for sparse bams)
- Add assembly of large-event breakends and basepair resolution SV reporting
- MANTA-19 Correctly parse large deletion reads from Isaac and incorporate this into discovery
- Fix sensitivity problems caused by unexpected proper pair bit settings, fix several self-edge issues. Detect intrachrom variants down to ~2kb.
- Expand POC calls to include intrachromosomal variants down to ~5kb.
- Minor modifications to method based on FFPE testing.
- POC somatic transloc output
- POC translation of graph into candidate transloc vcf
- working proof of concept denoised sv locus graph
- initial prototype code tag