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RELEASE_NOTES.html
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<h1 id="release-notes">RELEASE NOTES</h1>
<h2 id="0110">0.11.0</h2>
<p>This release introduce splice annotation tool, and update duckDB python package for improve stability.</p>
<h3 id="news">News</h3>
<ul>
<li>Add splice tool with docker image</li>
<li>Add plugins:
<ul>
<li>'genebe' (GeneBe annotation using REST API)</li>
<li>'minimalize' (Minimalize a VCF file, such as removing INFO/Tags or samples)</li>
</ul>
</li>
</ul>
<h3 id="updates">Updates</h3>
<ul>
<li>DuckDB 1.0.0 stable Snow Duck (Anas Nivis) release</li>
<li>Add API Documentation</li>
<li>Improve tests</li>
</ul>
<h3 id="fixes">Fixes</h3>
<ul>
<li>Paths parameters check fixed (genome and genomes-folders)</li>
<li>Fix snpEff download error with databases list</li>
</ul>
<h2 id="0100">0.10.0</h2>
<p>This release is a refactor of HOWARD (Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery) in Python, using Parquet and duckDB.</p>
<p>HOWARD annotates and prioritizes genetic variations, calculates and normalizes annotations, translates files in multiple formats (e.g. vcf, tsv, parquet) and generates variants statistics.</p>
<p>See <a href="README.md">README</a> and <a href="https://github.com/bioinfo-chru-strasbourg/howard">gitHub</a> for more explanations.</p>
<h2 id="previous-releases">Previous releases</h2>
<p>See <a href="https://github.com/bioinfo-chru-strasbourg/howard">HOWARD gitHub</a> for more information about previous releases.</p>
<h4 id="09b-07102016">0.9b-07/10/2016:</h4>
<ul>
<li>Script creation</li>
</ul>
<h4 id="091b-11102016">0.9.1b-11/10/2016:</h4>
<ul>
<li>Add Prioritization and Translation</li>
</ul>
<h4 id="091b-11102016">0.9.1b-11/10/2016:</h4>
<ul>
<li>Add snpEff annotation and stats</li>
</ul>
<h4 id="098b-21032017">0.9.8b-21/03/2017:</h4>
<ul>
<li>Add Multithreading on Prioritization and Translation</li>
</ul>
<h4 id="099b-18042017">0.9.9b-18/04/2017:</h4>
<ul>
<li>Add Calculation step</li>
</ul>
<h4 id="0910b-07112017">0.9.10b-07/11/2017:</h4>
<ul>
<li>Add generic file annotation through --annotation option</li>
<li>No need to be in configuration file</li>
<li>Need to be in ANNOVAR database folder (file 'ASSEMBLY_ANN.txt' for annotation 'ANN')</li>
<li>Add options: --force , --split</li>
<li>Add options for VCFanotation.pl: --show_annoataion, --show_annotations_full</li>
<li>Add database download option nowget in VCFanotation.pl</li>
<li>Fixes: multithreading, VAF calculation, configuration and check dependencies</li>
</ul>
<h4 id="0911b-07052018">0.9.11b-07/05/2018:</h4>
<ul>
<li>Replace VCFTOOLS command to BCFTOOLS command</li>
<li>Release added into the output VCF</li>
<li>Update SNPEff options</li>
<li>Add VARTYPE, CALLING_QUALITY and CALLING_QUALITY_EXPLODE option on calculation</li>
<li>Add description on calculations</li>
</ul>
<h4 id="09111b-14052018">0.9.11.1b-14/05/2018:</h4>
<ul>
<li>Improve VCF validation</li>
<li>Fix snpEff annotation bug</li>
</ul>
<h4 id="09112b-17082018">0.9.11.2b-17/08/2018:</h4>
<ul>
<li>Add --vcf input vcf file option</li>
<li>Create Output file directory automatically</li>
<li>Improve Multithreading</li>
</ul>
<h4 id="0912b-24082018">0.9.12b-24/08/2018:</h4>
<ul>
<li>Improve Multithreading</li>
<li>Input VCF compressed with BGZIP accepted</li>
<li>Output VCF compression level</li>
<li>Add VCF input sorting and multiallele split step (by default)</li>
<li>Add VCF input normalization step with option --norm</li>
<li>Bug fixes</li>
</ul>
<h4 id="0913b-04102018">0.9.13b-04/10/2018:</h4>
<ul>
<li>Multithreading improved</li>
<li>Change default output vcf</li>
<li>Input vcf without samples allowed</li>
<li>VCF Validation with contig check</li>
<li>Add multi VCF in input option</li>
<li>Add --annotate option for BCFTOOLS annotation with a VCF and TAG (beta)</li>
<li>Remove no multithreading part code to multithreading with 1 thread</li>
<li>Remove --multithreading parameter, only --thread parameter to deal with multithreading</li>
<li>Replace --filter and --format parameters by --prioritization and --translation parameters</li>
<li>Add snpeff options to VCFannotation.pl</li>
</ul>
<h4 id="0914b-21012019">0.9.14b-21/01/2019:</h4>
<ul>
<li>Reorganization of folders (bin, config, docs, toolbox...).</li>
<li>Improve Translation (TSV or VCF, sort on fields, selection of fields, filtering on fields), especially memory efficiency</li>
<li>Change Number/Type/Description of new INFO/FORMAT header generated</li>
<li>Remove snpEff option --snpeff and --snpeff_hgvs. SnpEff is used through --annotation option</li>
<li>Add '#' to the TAB/TSV delimiter format header</li>
<li>Update dbNSFP config annotation file script</li>
<li>Change default configuration files for annotation (add dbSNFP 3.5a, update mcap and regspintron) and prioritization</li>
<li>Bug fixed: file identification in annotation configuration</li>
<li>Bug fixed: calculation INFO fields header, snpeff parameters options on multithreading</li>
<li>Bug fixed: snpeff parameters in command line</li>
</ul>
<h4 id="0915b-19092019">0.9.15b-19/09/2019:</h4>
<ul>
<li>Rename HOWARD.sh to HOWARD.</li>
<li>Add --nomen_fields parameter and update NOMEN calculation.</li>
<li>Add --bcftools_stats and --stats parameter.</li>
<li>Change PZScore, PZFlag, PZComment and PZInfos generation, adding default PZ and all PZ filters.</li>
<li>Bug fixed: translation fields identification.</li>
</ul>
<h4 id="09151b-28052020">0.9.15.1b-28/05/2020:</h4>
<ul>
<li>Bug fixed: NOMEN calculation clear previous NOMEN values if using force option.</li>
</ul>
<h4 id="09152-12102020">0.9.15.2-12/10/2020:</h4>
<ul>
<li>Change --norm parameter by adding '--check-ref=s' in bcftools command.</li>
<li>Add --norm_options parameter.</li>
<li>force translation VCF by default.</li>
<li>Change VAF_stats and add DP_stats.</li>
</ul>
<h4 id="09154-11042021">0.9.15.4-11/04/2021:</h4>
<ul>
<li>Remove --snpeff_threads parameter (for snpEff 5.0e compatibility) and improve --snpeff_stats.</li>
<li>Add a check and rehead INFO fields if necessary (prevent some incorrect INFO header format).</li>
<li>Fix --compress parameter and add --index parameter.</li>
</ul>
<h4 id="09155-21072021">0.9.15.5-21/07/2021:</h4>
<ul>
<li>Add INFO description Type option, with autodetection.</li>
<li>Add prioritization mode 'VaRank'/'max' for score calculation.</li>
<li>Add calculation DP, AD, GQ and associated stats.</li>
<li>Fix INFO field type for VCF.</li>
</ul>
<h4 id="09156-16092021">0.9.15.6-16/09/2021:</h4>
<ul>
<li>Structural variant compatibility.</li>
<li>NOMEN extraction and generation improved, with --nomen_pattern option (only for SNV and InDel).</li>
<li>Improve translation with variant sorting.</li>
<li>Improve error catching.</li>
</ul>
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