- Parallel threaded variant linker.
- sample vcf file from vcflib
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specific position annotator for human genomics.
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Gaurav Sablok, IBCH, PAN, Poznan, Poland,
https://portal.ichb.pl/laboratory-of-genomics/.
Email: [email protected]
Prof. Luiza Handschuh
Email: [email protected].
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Usage: varlinker <COMMAND>
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
Instytut Chemii Bioorganicznej
Polskiej Akademii Nauk
ul. Noskowskiego 12/14 | 61-704, Poznań
Poland