[ { "id": "compare_vcfs_inDir_isec", "name": "Compare VCFs inDir(bcftools)", "description": "Compare several VCF files", "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": "custom", "commands": [ { "name": "compare_vcfs_inDir_isec", "cname": "Compare VCFs in Directory (bcftools)", "command": "bcftools isec", "category": "vcf_postprocess", "output_dir": "compare_vcfs_inDir_isec", "inputs": [ { "name": "vcfs", "type": "vcfs_dir", "list": true, "description": "vcf files must be bziped and tabix indexed " } ], "outputs": [ { "name": "sites", "type": "txt", "file": "sites.txt", "description": "Results of bcftools isec" }, { "name": "common", "type": "txt", "file": "common.txt", "description": "Common positions in all VCFs" }, { "name": "common_vcf", "type": "vcf.gz", "file": "common_only.vcf.gz", "description": "VCF of common positions in all VCFs" } ], "options": [ { "name": "compare_vcfs_inDir_QUAL", "type": "numeric", "value": 10, "min": 1, "max": "NA", "step": 1, "label": "Exclude snps with QUAL less than" }, { "name": "compare_vcfs_inDir_snponly", "prefix": null, "type": "checkbox", "value": true, "label": "Retain only snp variants : TYPE='snp' " } ] } ], "prepare_report_script": "compare_vcfs_inDir_isec.prepare.report.R", "prepare_report_outputs": [ "Venn_compare_vcfs_inDir_isec_mqc.png" ], "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" ], "vcftools": [ "The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330" ], "upsetr": [ "Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983-1992, 2014.doi: https:\/\/doi.org\/10.1109\/TVCG.2014.2346248" ] }, "yaml": "{\n id: compare_vcfs_inDir_isec,\n name: Compare VCFs inDir(bcftools),\n description: \"Compare several VCF files\",\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: \"custom\",\n commands:\n [\n {\n name: compare_vcfs_inDir_isec,\n cname: \"Compare VCFs in Directory (bcftools)\",\n command: bcftools isec,\n category: \"vcf_postprocess\",\n output_dir: compare_vcfs_inDir_isec,\n inputs: [{ name: vcfs, type: \"vcfs_dir\", list: true, description: \"vcf files must be bziped and tabix indexed \" }],\n outputs: [\n { name: sites, type: \"txt\" , file: \"sites.txt\", description: \"Results of bcftools isec\" },\n { name: common, type: \"txt\" , file: \"common.txt\", description: \"Common positions in all VCFs\" },\n { name: common_vcf, type: \"vcf.gz\" , file: \"common_only.vcf.gz\", description: \"VCF of common positions in all VCFs\" }\n ],\n options:\n [\n {\n name: compare_vcfs_inDir_QUAL,\n type: numeric,\n value: 10,\n min: 1,\n max: NA,\n step: 1,\n label: \"Exclude snps with QUAL less than\",\n },\n {\n name: compare_vcfs_inDir_snponly,\n prefix: ,\n type: checkbox,\n value: TRUE,\n label: \"Retain only snp variants : TYPE='snp' \",\n },\n ],\n },\n ],\n prepare_report_script: compare_vcfs_inDir_isec.prepare.report.R,\n prepare_report_outputs: [\n Venn_compare_vcfs_inDir_isec_mqc.png,\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 # ],\n # vcftools: [\n # \"apt-get install -y vcftools\"\n # ],\n # upsetr: [\n # 'Rscript -e ''install.packages(\"UpSetR\",Ncpus=8, clean=TRUE);library(\"UpSetR\")'''\n # ],\n # tabix: [\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 vcftools: [\n \"The Variant Call Format and VCFtools, Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert Handsaker, Gerton Lunter, Gabor Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin and 1000 Genomes Project Analysis Group, Bioinformatics, 2011 http:\/\/dx.doi.org\/10.1093\/bioinformatics\/btr330\"\n ],\n upsetr: [\n \"Alexander Lex, Nils Gehlenborg, Hendrik Strobelt, Romain Vuillemot, Hanspeter Pfister, UpSet: Visualization of Intersecting Sets, IEEE Transactions on Visualization and Computer Graphics (InfoVis '14), vol. 20, no. 12, pp. 1983-1992, 2014.doi: https:\/\/doi.org\/10.1109\/TVCG.2014.2346248\"\n ] \n }\n}\n" } ]