[
    {
        "id": "bcftools_vcfFile_stats",
        "name": "BCFtools VCF Stats",
        "description": "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.",
        "version": "1.17",
        "website": "https:\/\/samtools.github.io\/bcftools\/",
        "git": "https:\/\/github.com\/samtools\/bcftools",
        "documentation": "https:\/\/samtools.github.io\/bcftools\/howtos\/index.html",
        "article": "10.1093\/bioinformatics\/btr509",
        "multiqc": "bcftools",
        "commands": [
            {
                "name": "bcftools_vcfFile_stats",
                "cname": "BCFtools VCFFile Stats",
                "command": "bcftools stats",
                "category": "vcf_postprocess",
                "output_dir": "bcftools_vcfFile_stats",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf_file",
                        "file": "*_variants.vcf.gz",
                        "description": "Variant file (vcf)"
                    }
                ],
                "outputs": [
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "vcf_stats.txt",
                        "description": "VCF file stats"
                    },
                    {
                        "name": "stats_image",
                        "type": "png",
                        "file": "bcftools_stats_mqc.png",
                        "description": "VCF file stats graphs"
                    }
                ],
                "options": []
            }
        ],
        "install": [],
        "citations": {
            "bcftools": [
                "Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509"
            ],
            "tabix": [
                "Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718-719, https:\/\/doi.org\/10.1093\/bioinformatics\/btq671"
            ],
            "matplotlib": [
                "J. D. Hunter, 'Matplotlib: A 2D Graphics Environment,' in Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, May-June 2007, doi: 10.1109\/MCSE.2007.55."
            ]
        },
        "yaml": "{\n  id: \"bcftools_vcfFile_stats\",\n  name: \"BCFtools VCF Stats\",\n  description: \"BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.\",\n  version: \"1.17\",\n  website: \"https:\/\/samtools.github.io\/bcftools\/\",\n  git: \"https:\/\/github.com\/samtools\/bcftools\",\n  documentation: \"https:\/\/samtools.github.io\/bcftools\/howtos\/index.html\",\n  article: \"10.1093\/bioinformatics\/btr509\",\n  multiqc: \"bcftools\",\n  commands:\n    [\n      {\n        name: \"bcftools_vcfFile_stats\",\n        cname: \"BCFtools VCFFile Stats\",\n        command: \"bcftools stats\",\n        category: vcf_postprocess,\n        output_dir: \"bcftools_vcfFile_stats\",\n        inputs:\n          [\n            {\n              name: \"vcf\",\n              type: \"vcf_file\",\n              file: \"*_variants.vcf.gz\",\n              description: \"Variant file (vcf)\",\n            },\n          ],\n        outputs:\n          [\n            {\n              name: \"stats\",\n              type: \"txt\",\n              file: \"vcf_stats.txt\",\n              description: \"VCF file stats\",\n            },\n            {\n              name: \"stats_image\",\n              type: \"png\",\n              file: \"bcftools_stats_mqc.png\",\n              description: \"VCF file stats graphs\",\n            }\n          ],\n        options:\n          [\n          ],\n      },\n    ],\n  install:\n    {\n      # bcftools:\n      # [\n      #   \"cd \/opt\/biotools\",\n      #   \"wget https:\/\/github.com\/samtools\/bcftools\/releases\/download\/1.9\/bcftools-1.9.tar.bz2\",\n      #   \"tar -xvjf bcftools-1.9.tar.bz2\",\n      #   \"cd bcftools-1.9\",\n      #   \".\/configure --prefix=\/opt\/biotools\",\n      #   \"make -j 10\",\n      #   \"make install\",\n      #   \"mv bcftools \/opt\/biotools\/bin\/\",\n      #   \"cd .. && rm -r bcftools-1.9.tar.bz2 bcftools-1.9\",\n      #   \"sed -i 's\/python\/python3\/g' \/opt\/biotools\/bin\/plot-vcfstats\",\n      #   \"sed -i 's|11\/2.54|20\/2.54|' \/opt\/biotools\/bin\/plot-vcfstats\",\n      #   \"sed -i 's|10\/2.54|14\/2.54|' \/opt\/biotools\/bin\/plot-vcfstats\",\n      #   \"sed -i 's|window_len\/2|window_len\/\/2|g' \/opt\/biotools\/bin\/plot-vcfstats\"\n      # ],\n      # tabix:\n      # [\n      #   \"apt -y update && apt install -y tabix\"\n      # ],\n      # matplotlib:\n      # [\n      #   \"pip3 install matplotlib\"\n      # ],\n      # imagemagick:\n      # [\n      #   \"apt -y update && apt install -y imagemagick\"\n      # ],\n      # bcftools_dependencies: [\n      #   \"apt -y update && apt install -y python-backports.functools-lru-cache\"\n      # ]\n    },\n  citations:  {\n    bcftools: [\n      \"Heng Li, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, Volume 27, Issue 21, 1 November 2011, Pages 2987-2993, https:\/\/doi.org\/10.1093\/bioinformatics\/btr509\"\n    ],\n    tabix: [\n      \"Heng Li, Tabix: fast retrieval of sequence features from generic TAB-delimited files, Bioinformatics, Volume 27, Issue 5, 1 March 2011, Pages 718-719, https:\/\/doi.org\/10.1093\/bioinformatics\/btq671\"\n    ],\n    matplotlib: [\n      \"J. D. Hunter, 'Matplotlib: A 2D Graphics Environment,' in Computing in Science & Engineering, vol. 9, no. 3, pp. 90-95, May-June 2007, doi: 10.1109\/MCSE.2007.55.\"\n    ],\n  }\n}\n"
    }
]