{ "info": { "author": "Jeremy McRae", "author_email": "jmcrae@illumina.com", "bugtrack_url": null, "classifiers": [ "Development Status :: 4 - Beta", "License :: OSI Approved :: MIT License", "Topic :: Scientific/Engineering :: Bio-Informatics" ], "description": "#### vcfremapper\nutility to convert coordinates of variants in VCF files between different genome\nbuilds.\n\n### Install\nInstall via pip:\n```sh\npip install vcfremapper\n```\n\n### Usage\n``` sh\nvcfremapper PATH_TO_VCF CONVERTED --reference genome.fa\n\n# or pass output to bgzip\nvcfremapper PATH_TO_VCF --reference genome.fa | bgzip > CONVERTED\n\n# or pipe in gzipped data\ncat PATH_TO_VCF | vcfremapper --reference genome.fa | bgzip > CONVERTED\n```\n\nOptions:\n - `--reference` - path to reference genome, for the build being converted to.\n - `--build-in` - build to convert from, defaults to hg19\n - `--build-out` - build to convert to, defaults to hg38\n - `--tempdir` - folder to save uncompressed temp file in before 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