Updates - ACEnglish/truvari GitHub Wiki

Truvari 4.2.2

in progress

  • collapse
    • Fewer comparisons needed per-chunk on average
    • Fixed --chain functionality (details)
  • bench
    • Faster result at the cost of less complete annotations with --short flag
  • refine
    • Assures variants are sequence resolved before incorporating into consensus
    • bench --passonly --sizemax parameters are used when building consensus for a region. Useful for refine --use-original-vcfs
    • When a refined region has more than 5k variants, it is skipped and a warning of the region is written to the log
    • Flag --use-region-coords now expands --region coordinates by 100bp (phab --buffer default) to allow variants to harmonize out of regions.
  • general
    • Dynamic bed/vcf parsing tries to choose faster of streaming/fetching variants

Truvari 4.2.1

February 6, 2024

  • collapse
    • Faster handling of genotype data for --gt and --keep common
  • general
    • Fix to bed end position bug for including variants (details)
    • Fix to Dockerfile
  • refine
    • Changes to --recount that accompany the fix to bed end positions.
  • New command ga4gh to convert Truvari results into GA4GH truth/query VCFs with intermediates tags

Truvari 4.2

January 12, 2024

  • collapse
    • New parameter --gt disallows intra-sample events to collapse (details)
    • New parameter --intra for consolidating SAMPLE information during intra-sample collapsing (details)
    • Preserve phasing information when available
    • Faster O(n-1) algorithm instead of O(n^2)
    • Faster sub-chunking strategy makes smaller chunks of variants needing fewer comparisons
    • Fixed rare non-determinism error in cases where multiple variants are at the same position and equal qual/ac could be ordered differently.
  • phab
    • Correct sample handling with --bSamples --cSamples parameters
    • Faster generation of consensus sequence
    • Resolved 'overlapping' variant issue causing variants to be dropped
    • New poa approach to harmonization. Faster than mafft but less accurate. Slower than wfa but more accurate.
  • bench
    • New, easier MatchId field to track which baseline/comparison variants match up details
    • entry_is_present method now considers partial missing variants (e.g. ./1) as present
    • Removed the 'weighted' metrics from summary.json
  • consistency
    • Fixed issue with counting duplicate records
    • Added flag to optionally ignore duplicate records
  • anno svinfo now overwrites existing SVLEN/SVTYPE info fields
  • general
    • Reduced fn matches for unroll sequence similarity by reporting maximum of multiple manipulations of variant sequence (roll up/down/none). Comes at a small, but reasonable, expense of some more fp matches.
    • Bump pysam version
    • Fixed bug in unroll sequence similarity that sometimes rolled from the wrong end
    • Fixed bug for handling of None in ALT field
    • truvari.compress_index_vcf forces overwriting of tabix index to prevent annoying crashes

Truvari 4.1

August 7, 2023

  • bench
    • Creates candidate.refine.bed which hooks into refine on whole-genome VCFs details
    • --recount for correctly assessing whole-genome refinement results
    • experimental 'weighted' summary metrics details
    • Unresolved SVs (e.g. ALT == <DEL>) are filtered when --pctseq != 0
  • phab
    • ~2x faster via reduced IO from operating in stages instead of per-region
    • Removed most external calls (e.g. samtools doesn't need to be in the environment anymore)
    • new --align wfa allows much faster (but slightly less accurate) variant harmonization
    • increased determinism of results detals
  • refine
    • Faster bed file intersection of --includebed and --regions
    • Refine pre-flight check
    • Correct refine.regions.txt end position from IntervalTree correction
    • Better refine region selection with --use-original
    • --use-includebed switched to --use-region-coords so that default behavior is to prefer the includebed's coordinates
    • --use-original-vcfs to use the original pre-bench VCFs
    • refine.variant_summary.json is cleaned of uninformative metrics
  • stratify
    • parallel parsing of truvari directory to make processing ~4x faster
  • msa2vcf Fixed REPL decomposition bug to now preserve haplotypes
  • anno grpaf - expanded annotation info fields
  • anno density - new parameter --stepsize for sliding windows
  • collapse
    • New optional --median-info fields #146
  • Minor updates
    • Fix some anno threading on macOS #154
    • Monomorphic/multiallelic check fix in bench
    • PHAB_WRITE_MAFFT environment variable to facilitate updating functional test answer key
    • Slightly slimmer docker container

Truvari 4.0

March 13, 2023

As part of the GIAB TR effort, we have made many changes to Truvari's tooling to enable comparison of variants in TR regions down to 5bp. Additionally, in order to keep Truvari user friendly we have made changes to the UI. Namely, we've updated some default parameters, some command-line arguments, and some outputs. There are also a few new tools and how a couple of tools work has changed. Therefore, we decided to bump to a new major release. If you're using Truvari in any kind of production capacity, be sure to test your pipeline before moving to v4.0.

  • New refine command for refining benchmarking results. Details
  • bench
    • Unroll is now the default sequence comparison approach.
    • New --pick parameter to control the number of matches a variant can participate in details
    • The summary.txt is now named summary.json
    • Outputs parameters to params.json
    • Output VCFs are sorted, compressed, and indexed
    • Ambiguous use of 'call' in outputs corrected to 'comp' (e.g. tp-call.vcf.gz is now tp-comp.vcf.gz)
    • Renamed --pctsim parameter to --pctseq
    • Fixed bug where FP/FN weren't getting the correct, highest scoring match reported
    • Fixed bug where INFO/Multi wasn't being properly applied
    • Fixed bug where variants spanning exactly one --includebed region were erroneously being counted.
    • Removed parameters: --giabreport, --gtcomp,--multimatch, --use-lev, --prog, --unroll
  • collapse
    • Renamed --pctsim parameter to --pctseq
    • Runtime reduction by ~40% with short-circuiting during Matcher.build_match
    • Better output sorting which may allow pipelines to be a little faster.
  • vcf2df
    • More granular sizebins for [0,50) including better handling of SNPs
    • --multisample is removed. Now automatically add all samples with --format
    • key index column removed and replaced by chrom, start, end. Makes rows easier to read and easier to work with e.g. pyranges
  • anno
    • Simplified ui. Commands that work on a single VCF and can stream (stdin/stdout) no longer use --input but a positional argument.
    • Added addid
  • consistency
    • Slight speed improvement
    • Better json output format
  • segment
    • Added --passonly flag
    • Changed UI, including writing to stdout by default
    • Fixed END and 1bp DEL bugs, now adds N to segmented variants' REF, and info fields SVTYPE/SVLEN
  • API
    • Began a focused effort on improving re-usability of Truvari code.
    • Entry point to run benchmarking programmatically with Bench object.
    • Better development version tracking. details
    • Improved developer documentation. See readthedocs
  • general
    • msa2vcf now left-trims and decomposes variants into indels
    • Functional tests reorganization
    • Fix for off-by-one errors when using pyintervaltree. See ticket
    • Removed progressbar and Levenshtein dependencies as they are no longer used.

Truvari 3.5

August 27, 2022

  • bench
    • --dup-to-ins flag automatically treats SVTYPE==DUP as INS, which helps compare some programs/benchmarks
    • New --unroll sequence comparison method for bench and collapse (details)
  • Major anno trf refactor (TODO write docs) including:
    • annotation of DEL is fixed (was reporting the ALT copy numbers, not the sample's copy numbers after incorporating the ALT
    • allow 'denovo' annotation by applying any TRF annotations found, not just those with corresponding annotations
  • New anno grpaf annotates vcf with allele frequency info for groups of samples
  • New phab for variant harmonization (details)
  • backend
    • truvari.entry_size returns the length of the event in the cases where len(REF) == len(ALT) (e.g. SNPs entry_size is 1)
    • New key utility for truvari.build_anno_trees
  • general
    • Float metrics written to the VCF (e.g. PctSizeSimilarity) are rounded to precision of 4
    • Nice colors in some --help with rich
  • divide
    • output shards are now more easily sorted (i.e. ls divide_result/*.vcf.gz will return the shards in the order they were made)
    • compression/indexing of sub-VCFs in separate threads, reducing runtime
  • user issues
    • Monomorphic reference ALT alleles no longer throw an error in bench (#131)
    • SVLEN Number=A fix (#132)

Truvari 3.4

July 7, 2022

  • Improved performance of consistency (see #127)
  • Added optional json output of consistency report
  • Allow GT to be missing, which is allowed by VCF format specification
  • TRF now uses truvari.entry_variant_type instead of trying to use pysam.VariantRecord.info["SVLEN"] directly which allows greater flexibility.
  • vcf2df now parses fields with Number=\d (e.g. 2+), which is a valid description
  • truvari.seqsim is now case insensitive (see #128)
  • Collapse option to skip consolidation of genotype information so kept alleles are unaltered
  • truvari anno dpcnt --present will only count the depths of non ./. variants
  • New collapse annotation NumConsolidate records how many FORMATs were consolidated
  • Official conda support

Truvari 3.3

May 25, 2022

  • New utilities vcf_ranges and make_temp_filename
  • New annotations dpcnt and lcr
  • Fixed a bug in truvari collapse --keep that prevented the maxqual or common options from working
  • Increased determinism for truvari collapse so that in cases of tied variant position the longer allele is returned. If the alleles also have the same length, they are sorted alphabetically by the REF
  • New truvari bench --extend functionality. See discussion for details

Truvari 3.2

Apr 1, 2022

  • Removed truvari.copy_entry for pysam.VariantRecord.translate a 10x faster operation
  • Faster truvari collapse (@c8b319b)
  • When building MatchResult between variants with shared start/end positions, we save processing work by skipping haplotype creation and just compare REFs/ALTs directly.
  • Updated documentation to reference the paper https://doi.org/10.1101/2022.02.21.481353
  • New truvari anno density for identifying regions with 'sparse' and 'dense' overlapping SVs (details)
  • Better bench genotype reporting with summary.txt having a gt_matrix of Base GT x Comp GT for all Base calls' best, TP match.
  • New truvari anno bpovl for intersecting against tab-delimited files (details)
  • New truvari divide command to split VCFs into independent parts (details)
  • Replaced --buffer parameter with --minhaplen for slightly better matching specificity
  • Bugfix - truvari anno trf no longer duplicates entries spanning multple parallelization regions
  • Bugfix - collapse MatchId/CollapseId annotation wasn't working
  • Bugfixes - from wwliao (@4dd9968 @ef2cfb3)
  • Bugfixes - Issues #107, #108

Truvari 3.1

Dec 22, 2021

  • bench now annotates FPs by working a little differently. See bench for details.
  • Recalibrated TruScore and new reciprocal overlap measurement for sequence resolved INS (details)
  • Match objects are now usable via the SDK. See #94 for an example of using Truvari programmatically
  • file_zipper VCF iteration strategy (GenomeTree -> RegionVCFIterator) that improves speed, particularly when using --includebed
  • collapse refactored to use Match object and for prettier code, cleaner output.
  • anno remap now optionally adds INFO field of the location of the top N hits.
  • An experimental tool truvari segment added to help SV association analysis.
  • vcf2df now supports pulling FORMAT fields from multiple samples.
  • vcf2df now adds ('_ref', '_alt'), or ('_ref', '_het', '_hom') for INFO,Number=[R|G] fields, respectively.
  • Improved documentation, including http://truvari.readthedocs.io/ for developers.
  • Increasing/diversifying test coverage exposed minor bugs which were fixed.
  • bench --no-ref --cSample bug fixes.
  • Minor usability feature implemented in help_unknown_cmd.

Truvari 3.0

Sep 15, 2021

As Truvari's adoption and functionality grows, we decided to spend time working on sustainability and performance of the tool. Multiple Actions for CI/CD have been added. Many components have been refactored for speed, and other 'cruft' code has been removed. Some of these changes (particularly the switch to using edlib for sequence similarity) affects the results. Therefore, we've bumped to a new major release version.

  • Working on speed improvements
  • Added edlib as the default when calculating pctseq_sim, keeping Levenstein as an option (--use-lev).
  • truvari bench summary's gt_precision/gt_recall are replaced by gt_concordance, which is just the percent of TP-comp calls with a concordant genotype. --no-ref has better functionality. --giabreport is different.
  • Added —keep common to truvari collapse, which allows one to choose to keep the allele with the highest MAC.
  • truvari collapse --hap wasn't working correctly. The assumptions about the calls being phased wasn't being properly used (e.g. don't collapse 1|1) and the NumCollapsed was being populated before the single-best match was chosen. The latter is a reporting problem, but the former had an effect on the results with ~3% of collapsed calls being mis-collapsed.
  • truvari anno trf is now faster and simpler in its approach and whats reported.. and hopefully more useful.
  • truvari anno grm has min_size and regions arguments added.
  • truv2df has become truvari vcf2df where the default is vcf conversion with options to run on a truvari bench output directory. It also allows a specific sample to be parsed with --format and better Number=A handling.
  • NeighId added to truvari anno numneigh, which works like bedtools cluster.
  • The method af_calc now makes MAC/AC.
  • Added 'partial' to truvari anno remap.
  • Added truvari anno svinfo.
  • Removed truvari stats as truvari vcf2df is better and began building community-driven summaries.
  • Ubiquitous single version.
  • Added a Dockerfile and instructions for making a Truvari docker container.
  • Code and repository cleaning.
  • Github actions for automated pylint, testing, and releases to pypi.
  • Preserving per-version documentation from the wiki in docs/.

Truvari 2.1

Jan 27, 2021

We've expanded and improved Truvari's annotations. We've added an SV "collapsing" tool. And we've added a way to turn VCFs into pandas DataFrames easily for downstream analysis/QC.

Truvari 2.0

May 14, 2020

After performing a drastic code refactor, we were able to create several helper methods from Truvari's core functionality around SV comparisons and VCF manipulations. This reusable code gave us an opportunity to create tools relevant for SV analysis.

Truvari now contains multiple subcommands. In addition to the original benchmarking functionality (truvari bench), Truvari can generate SV relevant summary statistics, compute consistency of calls within VCFs, and we've begun to develop annotations for SVs. Details on these tools are on the WIKI.

We are committed to continually improving Truvari with the hopes of advancing the study and analysis of structural variation.

Truvari 1.3

September 25th, 2019

Truvari has some big changes. In order to keep up with the o deement of Python 2.7 https://pythonclock.org/ We're now only supporting Python 3.

Additionally, we now package Truvari so it and its dependencies can be installed directly. See Installation below. This will enable us to refactor the code for easier maintenance and reusability.

Finally, we now automatically report genotype comparisons in the summary stats.

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