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varlinker\n\n- Parallel threaded variant linker.\n- sample vcf file from [vcflib](https://github.com/vcflib/vcflib/blob/master/samples/sample.vcf)\n\n```\n__   __   __ _   _ __  | |     (_)  _ __   | | __   ___   _ __\n__   __   __ _   _ __  | |     (_)  _ __   | | __   ___   _ __\n\\ \\ / /  / _` | | '__| | |     | | | '_ \\  | |/ /  / _ \\ | '__|\n \\ V /  | (_| | | |    | |___  | | | | | | |   \u003c  |  __/ | |\n  \\_/    \\__,_| |_|    |_____| |_| |_| |_| |_|\\_\\  \\___| |_|\n\n\nspecific position annotator for human genomics.\n      ************************************************\n      Author Gaurav Sablok,\n      Email: codeprog@icloud.com\n     ************************************************\n\nUsage: varlinker \u003cCOMMAND\u003e\n\nCommands:\n variant-linker    annotate the specific coordinate\n variant-trefanno  extract the annotation of the specific ref allele\n variant-taltanno  extract the annotation of the specific alt allele\n help              Print this message or the help of the given subcommand(s)\n\nOptions:\n -h, --help     Print help\n -V, --version  Print version\n```\n\n- Annotate only the ref variant with A\n```\n./target/debug/varlinker variant-trefanno ./sample-files/sample.vcf A\n```\n\n- Annotate only the alt variant with A\n```\n./target/debug/varlinker variant-taltanno ./sample-files/sample.vcf T\n```\n- Annotate all the variants in the vcf\n```\n./target/debug/varlinker variant-linker ./sample-files/sample.vcf\n```\n\n- it will produce three output files classifying variant annotation to gene, exon and transcript level.\n\n```\n==\u003e annotationfile-exon.txt \u003c==\n19      111     .       A       C       exon    ENSG00000284900.2       KBTBD4\n19      111     .       A       C       exon    ENSG00000284900.2       KBTBD4\n19      111     .       A       C       exon    ENSG00000284900.2       KBTBD4\n19      111     .       A       C       exon    ENSG00000284900.2       KBTBD4\n\n==\u003e annotationfile-gene.txt \u003c==\n19      111     .       A       C       gene    ENSG00000284900.2       KBTBD4\n19      111     .       A       C       gene    ENSG00000278550.4       SLC43A2\n19      111     .       A       C       gene    ENSG00000264450.1       ENSG00000264450\n19      111     .       A       C       gene    ENSG00000273929.1       U6\n\n==\u003e annotationfile-transcript.txt \u003c==\n19      111     .       A       C       transcript      ENSG00000284900.2       KBTBD4\n19      111     .       A       C       transcript      ENSG00000284900.2       KBTBD4\n19      111     .       A       C       transcript      ENSG00000284900.2       KBTBD4\n19      111     .       A       C       transcript      ENSG00000284900.2       KBTBD4\n```\n\n- To install windows version:\n```\nrustup component add llvm-tools\nrustup target add x86_64-pc-windows-msvc\ngit clone https://github.com/IBCHgenomic/varlinker.git\ncd ensemblcov\ncargo xwin build --target x86_64-pc-windows-msvc\n```\n\nGaurav Sablok \\\ncodeprog@icloud.com\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fvarlinker","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frustcodepro%2Fvarlinker","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frustcodepro%2Fvarlinker/lists"}