[
    {
        "id": "bcftools_mpileup_and_call",
        "name": "BCFtools mpileup and call",
        "description": "BCFtools mpileup on each sample.",
        "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_mpileup_and_call",
                "cname": "BCFtools mpileup and call",
                "command": "bcftools",
                "category": "variant_calling",
                "output_dir": "bcftools_call",
                "inputs": [
                    {
                        "name": "bam",
                        "type": "bams",
                        "description": "Bam"
                    },
                    {
                        "name": "genome_fasta",
                        "type": "contigs",
                        "description": "Fasta reference",
                        "from": "parameter"
                    }
                ],
                "outputs": [
                    {
                        "name": "vcf",
                        "type": "vcf",
                        "file": "{sample}_variants.vcf.gz",
                        "description": "Variant file (vcf)"
                    },
                    {
                        "name": "stats",
                        "type": "txt",
                        "file": "{sample}_vcf_stats.txt",
                        "description": "VCF file stats"
                    }
                ],
                "options": [
                    {
                        "name": "bcftools_mpileup_and_call_threads",
                        "prefix": "--threads",
                        "value": 4,
                        "min": 1,
                        "max": 32,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "bcftools_mpileup_and_call_genome_fasta",
                        "type": "input_file",
                        "value": "",
                        "label": "Path to reference genome fasta file"
                    }
                ]
            }
        ],
        "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_mpileup_and_call\",\n  name: \"BCFtools mpileup and call\",\n  description: \"BCFtools mpileup on each sample.\",\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_mpileup_and_call\",\n        cname: \"BCFtools mpileup and call\",\n        command: \"bcftools\",\n        category: variant_calling,\n        output_dir: \"bcftools_call\",\n        inputs:\n          [\n            { name: \"bam\", type: \"bams\", description: \"Bam\" },\n            { name: \"genome_fasta\", type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" },\n          ],\n        outputs:\n          [\n            {\n              name: \"vcf\",\n              type: \"vcf\",\n              file: \"{sample}_variants.vcf.gz\",\n              description: \"Variant file (vcf)\",\n            },\n            {\n              name: \"stats\",\n              type: \"txt\",\n              file: \"{sample}_vcf_stats.txt\",\n              description: \"VCF file stats\",\n            }\n          ],\n        options:\n          [\n            {\n              name: \"bcftools_mpileup_and_call_threads\",\n              prefix: \"--threads\",\n              value: 4,\n              min: 1,\n              max: 32,\n              step: 1,\n              label: \"Threads to use\",\n              type: \"numeric\",\n            },\n            {\n              name: bcftools_mpileup_and_call_genome_fasta,\n              type: input_file,\n              value: \"\",\n              label: \"Path to reference genome fasta file\",\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}\n"
    }
]