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varlinker
Parallel threaded variant linker.
sample vcf file from vcflib
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specific position annotator for human genomics.
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Author Gaurav Sablok,
Email: codeprog@ icloud. com
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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
Gaurav Sablok codeprog@icloud.com