[
    {
        "id": "BEDTools_vcf_flanking_sequence",
        "name": "BEDTools vcf flanking sequence",
        "description": "BEDTools to obtain the flanking sequence of each variant in the VCF.",
        "version": "2.31",
        "website": "https:\/\/bedtools.readthedocs.io\/en\/latest\/",
        "git": "https:\/\/github.com\/arq5x\/bedtools2",
        "documentation": "https:\/\/bedtools.readthedocs.io\/en\/latest\/",
        "article": "doi: 10.1093\/bioinformatics\/btq033",
        "multiqc": "custom",
        "commands": [
            {
                "name": "BEDTools_vcf_flanking_sequence",
                "cname": "BEDTools vcf flanking sequence",
                "command": "bedtools",
                "category": "vcf_postprocess",
                "output_dir": "vcf_flanking_sequence",
                "inputs": [
                    {
                        "name": "vcf",
                        "type": "vcf_file",
                        "description": "Variant Calling Format (vcf) file"
                    },
                    {
                        "name": "genome_fasta",
                        "type": "fasta_file",
                        "description": "Fasta reference"
                    }
                ],
                "outputs": [
                    {
                        "name": "bed",
                        "type": "bed",
                        "file": "vcf_flanking.bed",
                        "description": "Bed"
                    },
                    {
                        "name": "fasta",
                        "type": "fasta_file",
                        "file": "vcf_flanking.fa",
                        "description": "flanking sequence fasta file of the variant (in vcf)"
                    }
                ],
                "options": [
                    {
                        "name": "BEDTools_vcf_flanking_sequence_threads",
                        "prefix": "--threads",
                        "value": 4,
                        "min": 1,
                        "max": 32,
                        "step": 1,
                        "label": "Threads to use",
                        "type": "numeric"
                    },
                    {
                        "name": "BEDTools_vcf_flanking_size",
                        "prefix": "",
                        "value": 100,
                        "min": 1,
                        "max": 500,
                        "step": 1,
                        "label": "Size of the flanking sequence upstream and downstream the variant",
                        "type": "numeric"
                    }
                ]
            }
        ],
        "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"
            ],
            "bedtools": [
                "Quinlan AR and Hall IM, BEDTools: : a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, 15 March 2010, Pages 841-842, doi: 10.1093\/bioinformatics\/btq033"
            ],
            "samtools": [
                "Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352"
            ]
        },
        "yaml": "{\n  id: \"BEDTools_vcf_flanking_sequence\",\n  name: \"BEDTools vcf flanking sequence\",\n  description: \"BEDTools to obtain the flanking sequence of each variant in the VCF.\",\n  version: \"2.31\",\n  website: \"https:\/\/bedtools.readthedocs.io\/en\/latest\/\",\n  git: \"https:\/\/github.com\/arq5x\/bedtools2\",\n  documentation: \"https:\/\/bedtools.readthedocs.io\/en\/latest\/\",\n  article: \"doi: 10.1093\/bioinformatics\/btq033\",\n  multiqc: \"custom\",\n  commands:\n    [\n      {\n        name: \"BEDTools_vcf_flanking_sequence\",\n        cname: \"BEDTools vcf flanking sequence\",\n        command: \"bedtools\",\n        category: vcf_postprocess,\n        output_dir: \"vcf_flanking_sequence\",\n        inputs:\n          [\n            { name: \"vcf\", type: \"vcf_file\", description: \"Variant Calling Format (vcf) file\" },\n            { name: \"genome_fasta\", type: \"fasta_file\", description: \"Fasta reference\" },\n          ],\n        outputs:\n          [\n            { name: \"bed\", type: \"bed\", file: \"vcf_flanking.bed\", description: \"Bed\" },\n            { name: \"fasta\", type: \"fasta_file\", file: \"vcf_flanking.fa\", description: \"flanking sequence fasta file of the variant (in vcf)\" }\n          ],\n        options:\n          [\n            {\n              name: \"BEDTools_vcf_flanking_sequence_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: BEDTools_vcf_flanking_size,\n              prefix: \"\",\n              value: 100,\n              min: 1,\n              max: 500,\n              step: 1,\n              label: \"Size of the flanking sequence upstream and downstream the variant\",\n              type: \"numeric\",\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    bedtools: [\n      \"Quinlan AR and Hall IM, BEDTools: : a flexible suite of utilities for comparing genomic features, Bioinformatics, Volume 26, Issue 6, 15 March 2010, Pages 841-842, doi: 10.1093\/bioinformatics\/btq033\"\n    ],\n    samtools: [\n      \"Heng Li, Bob Handsaker, Alec Wysoker, Tim Fennell, Jue Ruan, Nils Homer, Gabor Marth, Goncalo Abecasis, Richard Durbin, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment\/Map format and SAMtools, Bioinformatics, Volume 25, Issue 16, 15 August 2009, Pages 2078-2079, https:\/\/doi.org\/10.1093\/bioinformatics\/btp352\"\n    ]\n  }\n}\n"
    }
]