[ { "id": "bcftools_mpileup_and_call_onbam_dir", "name": "BCFtools mpileup and call jointly all bams in a dir", "description": "BCFtools mpileup is called jointly on all bams in a dir .", "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_onbam_dir", "cname": "BCFtools mpileup and call on bams dir", "command": "bcftools", "category": "variant_calling", "output_dir": "bcftools_call", "inputs": [ { "name": "bamDir", "type": "bams_dir", "description": "A directory containing Bam files one per sample" }, { "name": "genome_fasta", "type": "contigs", "description": "Fasta reference", "from": "parameter" } ], "outputs": [ { "name": "vcf", "type": "vcf_file", "file": "variants.vcf.gz", "description": "Variant file (vcf)" }, { "name": "stats", "type": "txt", "file": "vcf_stats.txt", "description": "VCF file stats" } ], "options": [ { "name": "bcftools_mpileup_and_call_onbam_dir_threads", "prefix": "--threads", "value": 4, "min": 1, "max": 64, "step": 1, "label": "Threads to use", "type": "numeric" }, { "name": "bcftools_mpileup_and_call_onbam_dir_genome_fasta", "type": "input_file", "value": "", "label": "Path to reference genome fasta file" }, { "name": "bcftools_mpileup_and_call_onbam_dir_minMeanDepth", "prefix": "", "value": 1, "min": 1, "max": 1000, "step": 1, "label": "Includes only sites with mean depth values (over all included individuals) greater than or equal to ", "type": "numeric" }, { "name": "bcftools_mpileup_and_call_onbam_dir_minctgSize", "prefix": "", "value": 1, "min": 1, "max": 10000000, "step": 10, "label": "Call variant for contigs with size greater than ", "type": "numeric" }, { "name": "bcftools_mpileup_and_call_onbam_dir_minmaf", "prefix": "--minmaf", "value": 0, "min": 0, "max": 1, "step": 0.01, "label": "Variant minor allel frequency to keep", "type": "numeric" }, { "name": "bcftools_mpileup_and_call_onbam_dir_missing", "prefix": "--missing", "value": 1, "min": 0, "max": 1, "step": 0.01, "label": "max missing snps(1 allows sites completely missing 0 no missing data allowed)", "type": "numeric" }, { "name": "bcftools_mpileup_and_call_onbam_dir_biallelicOnly", "prefix": "--biallelicOnly", "type": "checkbox", "value": false, "label": "Include only bi-allelic sites." }, { "name": "bcftools_mpileup_and_call_onbam_dir_snpOnly", "prefix": "--snpOnly", "type": "checkbox", "value": false, "label": "Include or exclude sites that contain an indel." } ] } ], "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_onbam_dir\",\n name: \"BCFtools mpileup and call jointly all bams in a dir\",\n description: \"BCFtools mpileup is called jointly on all bams in a dir .\",\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_onbam_dir\",\n cname: \"BCFtools mpileup and call on bams dir\",\n command: \"bcftools\",\n category: variant_calling,\n output_dir: \"bcftools_call\",\n inputs:\n [\n { name: \"bamDir\", type: \"bams_dir\", description: \"A directory containing Bam files one per sample\" },\n { name: \"genome_fasta\", type: \"contigs\", description: \"Fasta reference\", from: \"parameter\" },\n ],\n outputs:\n [\n {\n name: \"vcf\",\n type: \"vcf_file\",\n file: \"variants.vcf.gz\",\n description: \"Variant file (vcf)\",\n },\n {\n name: \"stats\",\n type: \"txt\",\n file: \"vcf_stats.txt\",\n description: \"VCF file stats\",\n }\n ],\n options:\n [\n {\n name: \"bcftools_mpileup_and_call_onbam_dir_threads\",\n prefix: \"--threads\",\n value: 4,\n min: 1,\n max: 64,\n step: 1,\n label: \"Threads to use\",\n type: \"numeric\",\n },\n {\n name: bcftools_mpileup_and_call_onbam_dir_genome_fasta,\n type: input_file,\n value: \"\",\n label: \"Path to reference genome fasta file\",\n },\n {\n name: \"bcftools_mpileup_and_call_onbam_dir_minMeanDepth\",\n prefix: \"\",\n value: 1,\n min: 1,\n max: 1000,\n step: 1,\n label: \"Includes only sites with mean depth values (over all included individuals) greater than or equal to \",\n type: \"numeric\",\n },\n {\n name: \"bcftools_mpileup_and_call_onbam_dir_minctgSize\",\n prefix: \"\",\n value: 1,\n min: 1,\n max: 10000000,\n step: 10,\n label: \"Call variant for contigs with size greater than \",\n type: \"numeric\",\n }, \n {\n name: \"bcftools_mpileup_and_call_onbam_dir_minmaf\",\n prefix: \"--minmaf\",\n value: 0,\n min: 0,\n max: 1,\n step: 0.01,\n label: \"Variant minor allel frequency to keep\",\n type: \"numeric\",\n }, \n {\n name: \"bcftools_mpileup_and_call_onbam_dir_missing\",\n prefix: \"--missing\",\n value: 1,\n min: 0,\n max: 1,\n step: 0.01,\n label: \"max missing snps(1 allows sites completely missing 0 no missing data allowed)\",\n type: \"numeric\",\n },\n { \n name: \"bcftools_mpileup_and_call_onbam_dir_biallelicOnly\",\n prefix: \"--biallelicOnly\",\n type: checkbox,\n value: FALSE,\n label: \"Include only bi-allelic sites.\",\n }, \n { \n name: \"bcftools_mpileup_and_call_onbam_dir_snpOnly\",\n prefix: \"--snpOnly\",\n type: checkbox,\n value: FALSE,\n label: \"Include or exclude sites that contain an indel.\",\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" } ]