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
)
- Filtered VCF files (
- From the WGS pipeline:
- Filtered VCF files (
variants-somatic.vcf.gz
)
- Filtered VCF files (
- From the Genotyping pipeline:
- OncoArray VCF files (
genotypes_all.vcf.gz
) - Imputed VCF files (
imputed_phase3_beagle.vcf.gz
)
- OncoArray VCF files (
The indexing and search functionality is provided by Apache Lucene.
Documentation
- BASE 3.19.12 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 | |
1.15 | 7804 | July 1, 2024 | varsearch-1.15.tar.gz (8.4MB) | 3.19.12 | changelog | |
1.14 | 7772 | June 18, 2024 | varsearch-1.14.tar.gz (8.4MB) | 3.19.12 | changelog | |
1.13 | 7738 | June 3, 2024 | varsearch-1.13.tar.gz (8.4MB) | 3.19.11 | changelog | |
1.12 | 7704 | May 14, 2024 | varsearch-1.12.tar.gz (8.4MB) | 3.19.10 | changelog | |
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 1.12 version:
svn co https://baseplugins.thep.lu.se/svn/extensions/net.sf.basedb.varsearch/tags/1.12 varsearch-1.12
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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Attachments (21)
-
varsearch-1.0-beta-1.tar.gz
(4.9 MB
) - added by 4 years ago.
Variant Search 1.0-beta-1
-
varsearch-1.0-beta-2.tar.gz
(5.0 MB
) - added by 4 years ago.
Variant Search 1.0-beta-2
-
varsearch-1.0-beta-3.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.0-beta-3
-
varsearch-1.0-beta-4.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.0-beta-4
-
varsearch-1.0-beta-5.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.0-beta-5
-
varsearch-1.0.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.0
-
varsearch-1.1.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.1
-
varsearch-1.2.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.2
-
varsearch-1.3.tar.gz
(5.0 MB
) - added by 3 years ago.
Variant Search 1.3
-
varsearch-1.4.tar.gz
(5.1 MB
) - added by 3 years ago.
Variant Search 1.4
-
varsearch-1.5.tar.gz
(5.1 MB
) - added by 3 years ago.
Variant Search 1.5
-
varsearch-1.6.tar.gz
(5.7 MB
) - added by 2 years ago.
Variant Search 1.6
-
varsearch-1.7.tar.gz
(5.7 MB
) - added by 2 years ago.
Variant Search 1.7
-
varsearch-1.8.tar.gz
(5.7 MB
) - added by 18 months ago.
Variant Search 1.8
-
varsearch-1.9.tar.gz
(6.6 MB
) - added by 13 months ago.
Variant Search 1.9
-
varsearch-1.10.tar.gz
(6.6 MB
) - added by 9 months ago.
Variant Search 1.10
-
varsearch-1.11.tar.gz
(8.4 MB
) - added by 5 months ago.
Variant Search 1.11
-
varsearch-1.12.tar.gz
(8.4 MB
) - added by 5 months ago.
Variant Search 1.12
-
varsearch-1.13.tar.gz
(8.4 MB
) - added by 4 months ago.
Variant Search 1.13
-
varsearch-1.14.tar.gz
(8.4 MB
) - added by 4 months ago.
Variant Search 1.14
-
varsearch-1.15.tar.gz
(8.4 MB
) - added by 3 months ago.
Variant Search 1.15