{
    "info": {
        "author": "Sander Bollen",
        "author_email": "a.h.b.bollen@lumc.nl",
        "bugtrack_url": null,
        "classifiers": [
            "License :: OSI Approved :: MIT License",
            "Programming Language :: Python :: 3.6",
            "Programming Language :: Python :: 3.7",
            "Programming Language :: Python :: 3 :: Only",
            "Topic :: Scientific/Engineering :: Bio-Informatics"
        ],
        "description": "vtools\n======\n\nLittle toolset operating over VCF files. Uses cyvcf2 and cython under\nthe hood for speed.\n\n\nTools\n-----\n\n### vtools-filter\n\nFilter VCF files based on a few criteria. Will output both a filtered VCF\nfile, and a VCF file containing all the filtered-out variants.\n\n####  Filter criteria\n\n| name | meaning | optional |\n| ---- | ------- | -------- |\n| NON_CANONICAL | Non-canonical chromosome | Yes |\n| INDEX_UNCALLED | Index uncalled or homozygous reference | Yes |\n| TOO_HIGH_GONL_AF | Too high GonL allele frequency | Yes |\n| TOO_HIGH_GNOMAD_AF | Too high GnomAD allele frequency | Yes |\n| LOW_GQ | Too low GQ on index sample | Yes |\n| DELETED_ALLELE | The only ALT allele is a deleted allele | No |\n\n#### Configuration \n\nConfiguration of filters goes by a little JSON file. \nSee [here](cfg/example-filter.json) for an example.\n\n\n#### Usage\n\n```bash\nUsage: vtools-filter [OPTIONS]\n\nOptions:\n  -i, --input PATH                Path to input VCF file  [required]\n  -o, --output PATH               Path to output (filtered) VCF file\n                                  [required]\n  -t, --trash PATH                Path to trash VCF file  [required]\n  -p, --params-file PATH          Path to filter params json  [required]\n  --index-sample TEXT             Name of index sample  [required]\n  --immediate-return / --no-immediate-return\n                                  Immediately write filters to file upon\n                                  hitting one filter criterium. Default = True\n  --help                          Show this message and exit.\n\n```\n\n### vtools-stats\n\nCollects some general statistics about a VCF file, and writes a json to\nstdout.\n\n#### Usage\n\n```bash\nUsage: vtools-stats [OPTIONS]\n\nOptions:\n  -i, --input FILE  Input VCF file  [required]\n  --help            Show this message and exit.\n```\n\n### vtools-gcoverage\n\nCollect coverage metrics over a gVCF file for every exon or every transcript\nin a refFlat file. This assumes the input VCF file is at least similar to\nGATK's gVCF files. gVCF files are only expected to have one sample; if\nyour input file contains multiple samples, we simply take the first only.\n\nOutput is a simple TSV file with the following columns\n\n| column | meaning |\n| ------ | ------- |\n| exon | exon number |\n| gene | gene name / symbol / id |\n| mean_dp | mean DP value over the exon |\n| mean_gq | mean GQ value over the exon* |\n| median_dp | median DP value over the exon |\n| median_gq | median GQ value over the exon |\n| perc_at_least_{10, 20, 30, 50, 100}_dp | Percentage of exon with DP value over value |\n| perc_at_least_{10, 29, 30, 50, 90}_gq | Percentage of exon with GQ value over exon | \n| transcript | transcript name / symbol / id |\n\n*: mean GQ value is computed by first calculating the P-value of all GQ \nvalues, then calculating the mean over these P-values, and lastly \nconverting this number back to a phred score.\n\n#### Usage\n\n```bash\nUsage: vtools-gcoverage [OPTIONS]\n\nOptions:\n  -I, --input-gvcf PATH          Path to input VCF file  [required]\n  -R, --refflat-file PATH        Path to refFlat file  [required]\n  --per-exon / --per-transcript  Collect metrics per exon or per transcript\n  --help                         Show this message and exit.\n```\n\n### vtools-evaluate\n\nEvaluate a VCF file to a baseline VCF file containing true positives. \nWe only consider variants that are present in both VCF files. This makes\nit useful when the two VCF files have been produced by wildly different\ntechnologies. E.g, when comparing a WES VCF file vs a SNP array, this\ntool can be quite useful.\n\nOutput is a simple JSON file listing counts of concordant and discordant\nalleles. \n\nMultisample VCF files are allowed; the samples to be evaluated have to be set \nthrough a CLI argument.\n\n\n#### Usage\n\n```bash\nUsage: vtools-evaluate [OPTIONS]\n\nOptions:\n  -c, --call-vcf PATH           Path to VCF with calls to be evaluated\n                                [required]\n  -p, --positive-vcf PATH       Path to VCF with known calls  [required]\n  -cs, --call-samples TEXT      Sample(s) in call-vcf to consider. May be\n                                called multiple times  [required]\n  -ps, --positive-samples TEXT  Sample(s) in positive-vcf to consider. May be\n                                called multiple times  [required]\n  --help                        Show this message and exit.\n```\n\n## Installation\n\nvtools is now on pip! Since the 'vtools' name is already taken by another\npackage, installing _this_ vtools requires installing the following:\n\n```bash\npip install v-tools\n```\n\nAfter installation, tools will still be called `vtools-<tool>`. Programmatic\naccess also simply works with\n\n```python\nimport vtools\n```\n\n## License\n\nMIT",
        "description_content_type": "",
        "docs_url": null,
        "download_url": "",
        "downloads": {
            "last_day": -1,
            "last_month": -1,
            "last_week": -1
        },
        "home_page": "https://git.lumc.nl/klinische-genetica/capture-lumc/vtools",
        "keywords": "",
        "license": "MIT",
        "maintainer": "",
        "maintainer_email": "",
        "name": "v-tools",
        "package_url": "https://pypi.org/project/v-tools/",
        "platform": "",
        "project_url": "https://pypi.org/project/v-tools/",
        "project_urls": {
            "Homepage": "https://git.lumc.nl/klinische-genetica/capture-lumc/vtools"
        },
        "release_url": "https://pypi.org/project/v-tools/1.0.0/",
        "requires_dist": null,
        "requires_python": ">=3.6",
        "summary": "Various tools operating over VCF files",
        "version": "1.0.0"
    },
    "last_serial": 5238560,
    "releases": {
        "1.0.0": [
            {
                "comment_text": "",
                "digests": {
                    "md5": "ae235fa1254fd94a0584814c294f86a9",
                    "sha256": "93db5295b6395034b92958b32d9398798489fb5dc7cef909e547a381b57a6458"
                },
                "downloads": -1,
                "filename": "v-tools-1.0.0.tar.gz",
                "has_sig": false,
                "md5_digest": "ae235fa1254fd94a0584814c294f86a9",
                "packagetype": "sdist",
                "python_version": "source",
                "requires_python": ">=3.6",
                "size": 142882,
                "upload_time": "2019-05-07T14:41:30",
                "url": "https://files.pythonhosted.org/packages/fd/40/61b0b5304947e3df2e409fc42a11cd03774953b1e0ebec356c8ccf49f81f/v-tools-1.0.0.tar.gz"
            }
        ]
    },
    "urls": [
        {
            "comment_text": "",
            "digests": {
                "md5": "ae235fa1254fd94a0584814c294f86a9",
                "sha256": "93db5295b6395034b92958b32d9398798489fb5dc7cef909e547a381b57a6458"
            },
            "downloads": -1,
            "filename": "v-tools-1.0.0.tar.gz",
            "has_sig": false,
            "md5_digest": "ae235fa1254fd94a0584814c294f86a9",
            "packagetype": "sdist",
            "python_version": "source",
            "requires_python": ">=3.6",
            "size": 142882,
            "upload_time": "2019-05-07T14:41:30",
            "url": "https://files.pythonhosted.org/packages/fd/40/61b0b5304947e3df2e409fc42a11cd03774953b1e0ebec356c8ccf49f81f/v-tools-1.0.0.tar.gz"
        }
    ]
}