Exomiser
rare-disease-wf
| Exomiser | rare-disease-wf | |
|---|---|---|
| 3 | 1 | |
| 181 | 56 | |
| 0.0% | - | |
| 8.9 | 0.0 | |
| 12 days ago | about 1 year ago | |
| Java | Nextflow | |
| GNU Affero General Public License v3.0 | MIT License |
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Exomiser
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I'm looking for a program to identify disease causing variants in a VCF file
That is not a trivial problem, even when you find a variant that could be causing the phenotype, a lot of evidence and expertise is required to validate that. There is not a single program or platform that can do that for you. But if you want to explore your data, there are VEP and Exomiser tools, but be aware those are not diagnostic tools.
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How to analyze your own raw genetic data for rare diseases/pathogenic markers/worst genes
Enter the Exomiser, an open source cross platform program to analyze your VCF file: https://github.com/exomiser/Exomiser The latest release as of this post is 12.1.0 and can be downloaded here: https://github.com/exomiser/Exomiser/releases/download/12.1.0/exomiser-cli-12.1.0-distribution.zip You also need to download the additional data here except for the hg19.zip: https://data.monarchinitiative.org/exomiser/latest/
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Is there a way to automatically classify variants as pathogenic?
VEP, Exomiser, Gemini, ...
rare-disease-wf
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Ask HN: How to be my own genetic disease researcher for my partner?
Feel free to reach out, username at berkeley edu.
In open source bioinformatics we strive for reproducible science, which can be difficult in a field with tons of different methods and tools. One approach is to use a workflow language such as Nextflow [0] and Docker/Singularity such that the entire analysis is reproducible, see e.g. [1].
There is a vibrant community around Nextflow workflows called nf-core [2] which has a rare disease workflow in development [3], come join our slack!
[0] - https://nextflow.io
[1] - https://github.com/brentp/rare-disease-wf
[2] - https://nf-co.re
[3] - https://nf-co.re/raredisease
What are some alternatives?
go-feature-flag - GO Feature Flag is a simple, complete and lightweight self-hosted feature flag solution 100% Open Source. 🎛️
slivar - genetic variant expressions, annotation, and filtering for great good.
SonarJava - :coffee: SonarSource Static Analyzer for Java Code Quality and Security
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
android-classyshark - Android and Java bytecode viewer
gnomad-browser - Explore gnomAD datasets on the web
BioJava - :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
octopus - Bayesian haplotype-based mutation calling
DNAnalyzer - Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
rnaseq-nf - A proof of concept of RNAseq pipeline
hlatyping - Precision HLA typing from next-generation sequencing data