- Parallel threaded variant linker.
- sample vcf file from vcflib
specific position annotator for human genomics.
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Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: gsablok@ibch.poznan.pl
Prof. Luiza Handschuh
Email: luizahan@ibch.poznan.pl.
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Usage: varlinker <COMMAND>
Commands:
variantlinker annotate the specific coordinate
variantrefanno extract the annotation of the specific ref allele
variantaltanno 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
- Acknowledgements: MOSAIC platform, developed as part of the ECBiG-MOSAIC project (POIR.04.02.00-00-D017/20), co-financed by the European Regional Development Fund (ERDF) under the Smart Growth Operational Programme 2014-2020, Measure 4.2 for the development of modern research infrastructure in the science sector.
- Project PI and Informal queries: Prof. Luiza Handschuh: luizahan@ibch.poznan.pl.
- Code related queries: Dr. Gaurav Sablok: gsablok@ibch.poznan.pl.
Gaurav Sablok Instytut Chemii Bioorganicznej Polskiej Akademii Nauk ul. Noskowskiego 12/14 | 61-704, Poznań Poland