Variant Search extension

This package is an extension package to BASE that implements a variant search engine for the variant calling results created be the Reggie variant calling pipeline. The search engine can also be used on the Relax server.

The search engine has support for the following:

• From the RNAseq pipeline:
  • Filtered VCF files (variants-filtered.vcf)
  • Raw annotated VCF files (variants-annotated.vcf)
  • Targeted genotyping files (genotype_*.vcf)
• From the WGS pipeline:
  • Filtered VCF files (variants-somatic.vcf.gz)
• From the Genotyping pipeline:
  • OncoArray VCF files (genotypes_all.vcf.gz)
  • Imputed VCF files (imputed_phase3_beagle.vcf.gz)

The indexing and search functionality is provided by Apache Lucene.

Documentation

• BASE 3.19.10 and Java 17 or higher is required.
• Installing
• How to use
• ​Apache Lucene homepage

License

​GNU Affero General Public License version 3

Download

Version	Revision	Date	Binary (tar.gz)	BASE Version*	Update notes
1.11	7695	May 6, 2024	varsearch-1.11.tar.gz​ (8.4MB)	3.19.10	Java 17!	changelog
1.10	7525	January 9, 2024	varsearch-1.10.tar.gz​ (6.6MB)	3.19.8		changelog
1.9	7306	August 28, 2023	varsearch-1.9.tar.gz​ (6.6MB)	3.19.8		changelog
1.8	7129	April 21, 2023	varsearch-1.8.tar.gz​ (5.7MB)	3.19.8		changelog
1.7	6850	October 21, 2022	varsearch-1.7.tar.gz​ (5.7MB)	3.19		changelog
1.6	6766	June 3, 2022	varsearch-1.6.tar.gz​ (5.7MB)	3.19		changelog
1.5	6570	February 2, 2022	varsearch-1.5.tar.gz​ (5.1MB)	3.18		changelog
1.4	6534	December 21, 2021	varsearch-1.4.tar.gz​ (5.1MB)	3.18		changelog
1.3	6417	September 20, 2021	varsearch-1.3.tar.gz​ (5.0MB)	3.18		changelog
1.2	6401	September 16, 2021	varsearch-1.2.tar.gz​ (5.0MB)	3.18		changelog
1.1	6287	June 11, 2021	varsearch-1.1.tar.gz​ (5.0MB)	3.18		changelog
1.0	6266	May 28, 2021	varsearch-1.0.tar.gz​ (5.0MB)	3.18		changelog

* In general, each release works with the specified and later BASE versions.

Source code can be downloaded from the subversion repository. Use the following command to get source code for the 1.6 version:

svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/tags/1.6 varsearch-1.6

The latest development (maybe unstable; do not use on a production server) revision can be checked out from the repository using the following command:

svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/trunk varsearch-dev

Contribute

After making modifications to the source code, compose a clear and concise log message to describe those changes and the reasons for them. Then, send an email to the developers list containing your log message and the output of svn diff (from the top of your subversion working copy). If the community members consider your changes acceptable, someone who has commit privileges will add your changes to the public source code tree. Recall that permission to directly commit changes to the repository is granted on merit - if you demonstrate comprehension of subversion, programming competency, and a team spirit, you will likely be awarded that permission.

Todo

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