[
    {
        "id": "bcftools_merge",
        "name": "Bcftools Merge VCFs",
        "article": "10.1093\/bioinformatics\/btr509",
        "website": "https:\/\/samtools.github.io\/bcftools\/bcftools.html",
        "git": "https:\/\/samtools.github.io\/bcftools\/",
        "description": "Merge multiple VCF or BCF files to create one multi-sample file combining compatible records into one",
        "version": "1.17",
        "documentation": "https:\/\/samtools.github.io\/bcftools\/bcftools.html#merge",
        "multiqc": "custom",
        "commands": [
            {
                "name": "bcftools_merge",
                "cname": "bcftools merge",
                "command": "",
                "category": "format_conversion",
                "output_dir": "bcftools_merge",
                "inputs": [
                    {
                        "name": "vcf_dir",
                        "type": "vcfs_dir"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf_file",
                        "type": "vcf_file",
                        "file": "merged.vcf.gz",
                        "description": "merged multisample vcf file"
                    }
                ],
                "options": [
                    {
                        "name": "bcftools_merge_force_samples",
                        "prefix": "",
                        "type": "checkbox",
                        "value": true,
                        "label": "If the merged files contain duplicate samples names, proceed anyway"
                    }
                ]
            }
        ],
        "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"
            ]
        },
        "yaml": "{\n  id: bcftools_merge,\n  name: Bcftools Merge VCFs,\n  article: \"10.1093\/bioinformatics\/btr509\",\n  website: \"https:\/\/samtools.github.io\/bcftools\/bcftools.html\",\n  git: \"https:\/\/samtools.github.io\/bcftools\/\",\n  description: \"Merge multiple VCF or BCF files to create one multi-sample file combining compatible records into one\",\n  version: \"1.17\",\n  documentation: \"https:\/\/samtools.github.io\/bcftools\/bcftools.html#merge\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: bcftools_merge,\n        cname: bcftools merge,\n        command: \"\",\n        category: \"format_conversion\",\n        output_dir: bcftools_merge,\n        inputs: [{ name: vcf_dir, type: \"vcfs_dir\" }],\n        outputs: [{ name: vcf_file, type: \"vcf_file\", file: \"merged.vcf.gz\", description: \"merged multisample vcf file\"}],\n        options: [\n         {\n            name: bcftools_merge_force_samples,\n            prefix: \"\",\n            type: checkbox,\n            value: True,\n            label: \"If the merged files contain duplicate samples names, proceed anyway\",\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      #   ],\n      # tabix:\n      #   [\n      #     \"apt -y update && apt install -y tabix\"\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  }\n}"
    }
]