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| # RELEASE NOTES | ||
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| ## 0.10.0 | ||
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| This release is a refactor of HOWARD (Highly Open Workflow for Annotation & Ranking toward genomic variant Discovery) in Python, using Parquet and duckDB. | ||
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| HOWARD annotates and prioritizes genetic variations, calculates and normalizes annotations, translates files in multiple formats (e.g. vcf, tsv, parquet) and generates variants statistics. | ||
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| See [README](README.md) and [gitHub](https://github.com/bioinfo-chru-strasbourg/howard) for more explanations. | ||
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| ## Previous releases | ||
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| See [HOWARD gitHub](https://github.com/bioinfo-chru-strasbourg/howard) for more information about previous releases. | ||
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| #### 0.9b-07/10/2016: | ||
| - Script creation | ||
| #### 0.9.1b-11/10/2016: | ||
| - Add Prioritization and Translation | ||
| #### 0.9.1b-11/10/2016: | ||
| - Add snpEff annotation and stats | ||
| #### 0.9.8b-21/03/2017: | ||
| - Add Multithreading on Prioritization and Translation | ||
| #### 0.9.9b-18/04/2017: | ||
| - Add Calculation step | ||
| #### 0.9.10b-07/11/2017: | ||
| - Add generic file annotation through --annotation option | ||
| - No need to be in configuration file | ||
| - Need to be in ANNOVAR database folder (file 'ASSEMBLY_ANN.txt' for annotation 'ANN') | ||
| - Add options: --force , --split | ||
| - Add options for VCFanotation.pl: --show_annoataion, --show_annotations_full | ||
| - Add database download option nowget in VCFanotation.pl | ||
| - Fixes: multithreading, VAF calculation, configuration and check dependencies | ||
| #### 0.9.11b-07/05/2018: | ||
| - Replace VCFTOOLS command to BCFTOOLS command | ||
| - Release added into the output VCF | ||
| - Update SNPEff options | ||
| - Add VARTYPE, CALLING_QUALITY and CALLING_QUALITY_EXPLODE option on calculation | ||
| - Add description on calculations | ||
| #### 0.9.11.1b-14/05/2018: | ||
| - Improve VCF validation | ||
| - Fix snpEff annotation bug | ||
| #### 0.9.11.2b-17/08/2018: | ||
| - Add --vcf input vcf file option | ||
| - Create Output file directory automatically | ||
| - Improve Multithreading | ||
| #### 0.9.12b-24/08/2018: | ||
| - Improve Multithreading | ||
| - Input VCF compressed with BGZIP accepted | ||
| - Output VCF compression level | ||
| - Add VCF input sorting and multiallele split step (by default) | ||
| - Add VCF input normalization step with option --norm | ||
| - Bug fixes | ||
| #### 0.9.13b-04/10/2018: | ||
| - Multithreading improved | ||
| - Change default output vcf | ||
| - Input vcf without samples allowed | ||
| - VCF Validation with contig check | ||
| - Add multi VCF in input option | ||
| - Add --annotate option for BCFTOOLS annotation with a VCF and TAG (beta) | ||
| - Remove no multithreading part code to multithreading with 1 thread | ||
| - Remove --multithreading parameter, only --thread parameter to deal with multithreading | ||
| - Replace --filter and --format parameters by --prioritization and --translation parameters | ||
| - Add snpeff options to VCFannotation.pl | ||
| #### 0.9.14b-21/01/2019: | ||
| - Reorganization of folders (bin, config, docs, toolbox...). | ||
| - Improve Translation (TSV or VCF, sort on fields, selection of fields, filtering on fields), especially memory efficiency | ||
| - Change Number/Type/Description of new INFO/FORMAT header generated | ||
| - Remove snpEff option --snpeff and --snpeff_hgvs. SnpEff is used through --annotation option | ||
| - Add '#' to the TAB/TSV delimiter format header | ||
| - Update dbNSFP config annotation file script | ||
| - Change default configuration files for annotation (add dbSNFP 3.5a, update mcap and regspintron) and prioritization | ||
| - Bug fixed: file identification in annotation configuration | ||
| - Bug fixed: calculation INFO fields header, snpeff parameters options on multithreading | ||
| - Bug fixed: snpeff parameters in command line | ||
| #### 0.9.15b-19/09/2019: | ||
| - Rename HOWARD.sh to HOWARD. | ||
| - Add --nomen_fields parameter and update NOMEN calculation. | ||
| - Add --bcftools_stats and --stats parameter. | ||
| - Change PZScore, PZFlag, PZComment and PZInfos generation, adding default PZ and all PZ filters. | ||
| - Bug fixed: translation fields identification. | ||
| #### 0.9.15.1b-28/05/2020: | ||
| - Bug fixed: NOMEN calculation clear previous NOMEN values if using force option. | ||
| #### 0.9.15.2-12/10/2020: | ||
| - Change --norm parameter by adding '--check-ref=s' in bcftools command. | ||
| - Add --norm_options parameter. | ||
| - force translation VCF by default. | ||
| - Change VAF_stats and add DP_stats. | ||
| #### 0.9.15.4-11/04/2021: | ||
| - Remove --snpeff_threads parameter (for snpEff 5.0e compatibility) and improve --snpeff_stats. | ||
| - Add a check and rehead INFO fields if necessary (prevent some incorrect INFO header format). | ||
| - Fix --compress parameter and add --index parameter. | ||
| #### 0.9.15.5-21/07/2021: | ||
| - Add INFO description Type option, with autodetection. | ||
| - Add prioritization mode 'VaRank'/'max' for score calculation. | ||
| - Add calculation DP, AD, GQ and associated stats. | ||
| - Fix INFO field type for VCF. | ||
| #### 0.9.15.6-16/09/2021: | ||
| - Structural variant compatibility. | ||
| - NOMEN extraction and generation improved, with --nomen_pattern option (only for SNV and InDel). | ||
| - Improve translation with variant sorting. | ||
| - Improve error catching. |