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        "author": "Sander Bollen",
        "author_email": "a.h.b.bollen@lumc.nl",
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        "description": "GVCF2BED\n========\n\nThis is a small tool to convert a gVCF file to BED. This is useful for\nextracting regions that pass a certain genotype quality threshold.\n\nInstallation\n------------\n\ngvcf2bed is now available through pypi with: ``pip install gvcf2bed``\n\nRequirements\n------------\n\n-  Python 3.4+\n-  pyvcf\n-  cyvcf2\n\nFor developers\n~~~~~~~~~~~~~~\n\n-  pytest\n-  pytest-cov\n\nChangelog\n---------\n\n0.3.1\n~~~~~\n\n-  Fix a bug for variants where GQ is not defined.\n\n0.3\n~~~\n\n-  Use ``cyvcf2`` by default in tool. This results in a speed-up of\n   approximately 8-10x. Existing API has not changed, and will still\n   work with ``pyvcf``.\n-  Add separate filter for non-variants, as GQ scores may have a\n   different distribution on non-variant records than on variant\n   records.\n\nUsage\n-----\n\n::\n\n    usage: gvcf2bed [-h] -I INPUT -O OUTPUT [-s SAMPLE] [-q QUALITY]\n                    [-nq NON_VARIANT_QUALITY] [-b]\n\n    Create a BED file from a gVCF. Regions are based on a minimum genotype\n    quality. The gVCF file must contain a GQ field in its FORMAT fields. GQ scores\n    of non-variants records have a different distribution from the GQ score\n    distribution of variant records. Hence, an option is provided to set a\n    different threshold for non-variant positions.\n\n    optional arguments:\n      -h, --help            show this help message and exit\n      -I INPUT, --input INPUT\n                            Input gVCF\n      -O OUTPUT, --output OUTPUT\n                            Output bed file\n      -s SAMPLE, --sample SAMPLE\n                            Sample name in VCF file to use. Will default to first\n                            sample (alphabetically) if not supplied\n      -q QUALITY, --quality QUALITY\n                            Minimum genotype quality (default 20)\n      -nq NON_VARIANT_QUALITY, --non-variant-quality NON_VARIANT_QUALITY\n                            Minimum genotype quality for non-variant records\n                            (default 20)\n      -b, --bedgraph        Output in bedgraph mode\n\n\n\n",
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        "license": "MIT",
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        "name": "gvcf2bed",
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