https://github.com/rustcodepro/varlinker
exact point variant annotation
https://github.com/rustcodepro/varlinker
bioinformatics variant-annotations variant-calling variant-effect-prediction variant-prioritization
Last synced: about 2 months ago
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exact point variant annotation
- Host: GitHub
- URL: https://github.com/rustcodepro/varlinker
- Owner: rustcodepro
- License: mpl-2.0
- Created: 2025-06-06T13:47:56.000Z (8 months ago)
- Default Branch: main
- Last Pushed: 2025-09-29T12:01:49.000Z (4 months ago)
- Last Synced: 2025-11-29T20:17:26.501Z (about 2 months ago)
- Topics: bioinformatics, variant-annotations, variant-calling, variant-effect-prediction, variant-prioritization
- Language: Rust
- Homepage:
- Size: 136 KB
- Stars: 0
- Watchers: 0
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# varlinker
- Parallel threaded variant linker.
- sample vcf file from [vcflib](https://github.com/vcflib/vcflib/blob/master/samples/sample.vcf)
```
__ __ __ _ _ __ | | (_) _ __ | | __ ___ _ __
__ __ __ _ _ __ | | (_) _ __ | | __ ___ _ __
\ \ / / / _` | | '__| | | | | | '_ \ | |/ / / _ \ | '__|
\ V / | (_| | | | | |___ | | | | | | | < | __/ | |
\_/ \__,_| |_| |_____| |_| |_| |_| |_|\_\ \___| |_|
specific position annotator for human genomics.
************************************************
Author Gaurav Sablok,
Email: codeprog@icloud.com
************************************************
Usage: varlinker
Commands:
variant-linker annotate the specific coordinate
variant-trefanno extract the annotation of the specific ref allele
variant-taltanno extract the annotation of the specific alt allele
help Print this message or the help of the given subcommand(s)
Options:
-h, --help Print help
-V, --version Print version
```
- Annotate only the ref variant with A
```
./target/debug/varlinker variant-trefanno ./sample-files/sample.vcf A
```
- Annotate only the alt variant with A
```
./target/debug/varlinker variant-taltanno ./sample-files/sample.vcf T
```
- Annotate all the variants in the vcf
```
./target/debug/varlinker variant-linker ./sample-files/sample.vcf
```
- it will produce three output files classifying variant annotation to gene, exon and transcript level.
```
==> annotationfile-exon.txt <==
19 111 . A C exon ENSG00000284900.2 KBTBD4
19 111 . A C exon ENSG00000284900.2 KBTBD4
19 111 . A C exon ENSG00000284900.2 KBTBD4
19 111 . A C exon ENSG00000284900.2 KBTBD4
==> annotationfile-gene.txt <==
19 111 . A C gene ENSG00000284900.2 KBTBD4
19 111 . A C gene ENSG00000278550.4 SLC43A2
19 111 . A C gene ENSG00000264450.1 ENSG00000264450
19 111 . A C gene ENSG00000273929.1 U6
==> annotationfile-transcript.txt <==
19 111 . A C transcript ENSG00000284900.2 KBTBD4
19 111 . A C transcript ENSG00000284900.2 KBTBD4
19 111 . A C transcript ENSG00000284900.2 KBTBD4
19 111 . A C transcript ENSG00000284900.2 KBTBD4
```
- To install windows version:
```
rustup component add llvm-tools
rustup target add x86_64-pc-windows-msvc
git clone https://github.com/IBCHgenomic/varlinker.git
cd ensemblcov
cargo xwin build --target x86_64-pc-windows-msvc
```
Gaurav Sablok \
codeprog@icloud.com