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RELEASE_NOTES.html
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<meta charset="utf-8" />
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<title>HOWARD RELEASE NOTES</title>
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<h1 class="title">HOWARD RELEASE NOTES</h1>
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<h1 data-number="1" id="release-notes"><span
class="header-section-number">1</span> RELEASE NOTES</h1>
<h2 data-number="1.1" id="section"><span
class="header-section-number">1.1</span> 0.12.0</h2>
<p>This release introduce ‘BigWig’ annotation, prioritization options
and transcripts view, improve samples managment, INFO/tags rename,
annotation databases generation and operations, confugation files in
YAML format, and python packages stability.</p>
<h3 data-number="1.1.1" id="news"><span
class="header-section-number">1.1.1</span> News</h3>
<ul>
<li>Add annotation method ‘BigWig’</li>
<li>Add prioritization options:
<ul>
<li>SQL syntax available to define filters</li>
<li>New ‘Class’ priorisation field</li>
</ul></li>
<li>New transcripts view:
<ul>
<li>Create a transcript view, using a structure from multiple source
type (e.g. snpEff, external annotation databases)</li>
<li>Mapping between multiple transcript ID source (e.g. refSeq,
Ensembl)</li>
<li>Transcripts prioritization, using same prioritization process than
variants</li>
<li>Export transcripts table as a file, in multiple format such as VCF,
TSV, Parquet</li>
</ul></li>
<li>Export with a specific sample list</li>
<li>Rename or remove INFO/tags before exporting</li>
<li>Configuration and parameters files in YAML format allowed</li>
<li>Add dynamic transcript column for NOMEN calculation (using
transcript priorization column)</li>
<li>Add plugins:
<ul>
<li>‘update_databases’</li>
</ul></li>
</ul>
<h3 data-number="1.1.2" id="updates"><span
class="header-section-number">1.1.2</span> Updates</h3>
<ul>
<li>Improve snpEff annotations operations</li>
<li>New option ‘uniquify’ for dbSNFP generation, identification of
columns type</li>
<li>Managment, check and export of samples columns</li>
<li>Improve query type mode</li>
<li>Improve splice annotation</li>
<li>Improve NOMEN generation</li>
</ul>
<h3 data-number="1.1.3" id="fixes"><span
class="header-section-number">1.1.3</span> Fixes</h3>
<ul>
<li>Genotype format detection</li>
<li>Fix packages releases</li>
<li>Fix parameters and configuration files options</li>
<li>Fix calculations list and parametrization</li>
<li>Fix empty file export</li>
<li>Fix BED annotation with parquet method</li>
<li>More explicite log messages</li>
</ul>
<h2 data-number="1.2" id="section-1"><span
class="header-section-number">1.2</span> 0.11.0</h2>
<p>This release introduce splice annotation tool, and update duckDB
python package for improve stability.</p>
<h3 data-number="1.2.1" id="news-1"><span
class="header-section-number">1.2.1</span> 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 data-number="1.2.2" id="updates-1"><span
class="header-section-number">1.2.2</span> 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 data-number="1.2.3" id="fixes-1"><span
class="header-section-number">1.2.3</span> Fixes</h3>
<ul>
<li>Paths parameters check fixed (genome and genomes-folders)</li>
<li>Fix snpEff download error with databases list</li>
</ul>
<h2 data-number="1.3" id="section-2"><span
class="header-section-number">1.3</span> 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.html">README</a> and <a
href="https://github.com/bioinfo-chru-strasbourg/howard">gitHub</a> for
more explanations.</p>
<h2 data-number="1.4" id="previous-releases"><span
class="header-section-number">1.4</span> 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 data-number="1.4.0.1" id="b-07102016"><span
class="header-section-number">1.4.0.1</span> 0.9b-07/10/2016:</h4>
<ul>
<li>Script creation #### 0.9.1b-11/10/2016:</li>
<li>Add Prioritization and Translation #### 0.9.1b-11/10/2016:</li>
<li>Add snpEff annotation and stats #### 0.9.8b-21/03/2017:</li>
<li>Add Multithreading on Prioritization and Translation ####
0.9.9b-18/04/2017:</li>
<li>Add Calculation step #### 0.9.10b-07/11/2017:</li>
<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 #### 0.9.11b-07/05/2018:</li>
<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 #### 0.9.11.1b-14/05/2018:</li>
<li>Improve VCF validation</li>
<li>Fix snpEff annotation bug #### 0.9.11.2b-17/08/2018:</li>
<li>Add –vcf input vcf file option</li>
<li>Create Output file directory automatically</li>
<li>Improve Multithreading #### 0.9.12b-24/08/2018:</li>
<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 #### 0.9.13b-04/10/2018:</li>
<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 #### 0.9.14b-21/01/2019:</li>
<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 ####
0.9.15b-19/09/2019:</li>
<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. ####
0.9.15.1b-28/05/2020:</li>
<li>Bug fixed: NOMEN calculation clear previous NOMEN values if using
force option. #### 0.9.15.2-12/10/2020:</li>
<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. #### 0.9.15.4-11/04/2021:</li>
<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. ####
0.9.15.5-21/07/2021:</li>
<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. #### 0.9.15.6-16/09/2021:</li>
<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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