rare-disease-wf
Exomiser
Our great sponsors
| rare-disease-wf | Exomiser | |
|---|---|---|
| 1 | 3 | |
| 56 | 180 | |
| - | 2.8% | |
| 0.0 | 9.0 | |
| about 1 year ago | about 2 months ago | |
| Nextflow | Java | |
| MIT License | GNU Affero General Public License v3.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
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
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, ...
What are some alternatives?
slivar - genetic variant expressions, annotation, and filtering for great good.
go-feature-flag - GO Feature Flag is a simple, complete and lightweight self-hosted feature flag solution 100% Open Source. 🎛️
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
SonarJava - :coffee: SonarSource Static Analyzer for Java Code Quality and Security
gnomad-browser - Explore gnomAD datasets on the web
android-classyshark - Android and Java bytecode viewer
octopus - Bayesian haplotype-based mutation calling
BioJava - :book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.
rnaseq-nf - A proof of concept of RNAseq pipeline
DNAnalyzer - Revolutionizing DNA analysis and making it accessible to all through innovative AI-powered analysis and interpretive tools
hlatyping - Precision HLA typing from next-generation sequencing data