Structural variant toolkit for VCFs
Minor bug fixes for collapse
and accuracy/speed improvements for refine
.
Full Updates: https://github.com/ACEnglish/truvari/wiki/Updates Full Changelog: https://github.com/ACEnglish/truvari/compare/v4.2.1...v4.2.2
ga4gh
commandFull Changelog: https://github.com/ACEnglish/truvari/compare/v4.2.0...v4.2.1
The main change to Truvari v4.2 is a major improvement to the speed and accuracy of truvari collapse
.
Other changes include various bug fixes and improvements to the bench, phab, and refine workflow.
Several minor quality of life fixes.
Full Updates: https://github.com/ACEnglish/truvari/wiki/Updates Full Changelog: https://github.com/ACEnglish/truvari/compare/v4.1.0...v4.2.0
Highlights:
truvari refine
on whole-genome benchmarkingtruvari phab
and truvari refine
Full updates: https://github.com/ACEnglish/truvari/wiki/updates#truvari-41 Full Changelog: https://github.com/ACEnglish/truvari/compare/v4.0.0...v4.1.0
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.
Highlighted Changes
Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.5.1...v4.0.0
This should be the last minor revision of v3. We're freezing this in order to preserve the SV >=50bp focused functionality.
bench --dup-to-ins
flag automatically treats SVTYPE==DUP as INS, which helps compare some programs/benchmarksanno grpaf
annotates vcf with allele frequency info for groups of samplesSee Wiki for full description of changes. Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.4.0...v3.5.0
Truvari is now officially on conda! Plus a new, faster truvari consistency
. And, as always there are minor bug fixes and small, backwards compatible, improvements.
See Updates for full details
create_file_intersections()
to save memory by @pwwang in https://github.com/ACEnglish/truvari/pull/126
Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.3.0...v3.4.0
Full Changelog: https://github.com/ACEnglish/truvari/compare/v3.2.0...v3.3.0
truvari.copy_entry
for pysam.VariantRecord.translate
a 10x faster operationtruvari collapse
(@c8b319b)MatchResult
between variants with shared start/end positions, we save processing work by skipping haplotype creation and just compare REFs/ALTs directly.truvari anno density
for identifying regions with 'sparse' and 'dense' overlapping SVs (details)bench
genotype reporting with summary.txt
having a gt_matrix
of Base GT x Comp GT for all Base calls' best, TP match.truvari anno bpovl
for intersecting against tab-delimited files (details)truvari divide
command to split VCFs into independent parts (details)--buffer
parameter with --minhaplen
for slightly better matching specificitytruvari anno trf
no longer duplicates entries spanning multple parallelization regionscollapse
MatchId/CollapseId annotation wasn't workingFull Changelog: https://github.com/spiralgenetics/truvari/compare/v3.0.1...v3.1.0