[ { "id": "gatk3_haplotype_caller", "name": "GATK3 Haplotype Caller", "article": "10.1101\/gr.107524.110", "website": "https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.8-0\/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php", "git": "", "description": "The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region", "version": "3.8", "documentation": "https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.8-0\/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php", "multiqc": "bcftools", "commands": [ { "name": "gatk3_haplotype_caller", "command": "gatk3", "category": "variant_calling", "output_dir": "gatk3_haplotype_caller", "inputs": [ { "name": "bams", "type": "bams" }, { "name": "genome_fasta", "type": "contigs" }, { "name": "fasta_index", "type": "fasta_index" }, { "name": "sequence_dict", "type": "sequence_dict" } ], "outputs": [ { "name": "vcf", "type": "vcf", "file": "{sample}_variants.vcf.gz", "description": "Variants file" }, { "name": "stats", "type": "txt", "file": "{sample}_vcf_stats.txt", "description": "VCF stats" } ], "options": [ { "name": "gatk3_haplotype_caller_threads", "type": "numeric", "value": 4, "min": 1, "max": "NA", "step": 1, "label": "Number of threads to use" }, { "name": "gatk3_haplotype_caller_genome_fasta", "type": "input_file", "value": "", "label": "Path to reference genome fasta file" } ] } ], "install": [], "citations": { "gatk": [ "McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297\u20111303. https:\/\/doi.org\/10.1101\/gr.107524.110 " ], "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" ], "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: gatk3_haplotype_caller,\n name: GATK3 Haplotype Caller,\n article: 10.1101\/gr.107524.110,\n website: \"https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.8-0\/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php\",\n git: \"\",\n description: \"The HaplotypeCaller is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region\",\n version: \"3.8\",\n documentation: \"https:\/\/software.broadinstitute.org\/gatk\/documentation\/tooldocs\/3.8-0\/org_broadinstitute_gatk_tools_walkers_haplotypecaller_HaplotypeCaller.php\",\n multiqc: \"bcftools\",\n commands:\n [\n {\n name: gatk3_haplotype_caller,\n command: gatk3,\n category: variant_calling,\n output_dir: gatk3_haplotype_caller,\n inputs: [\n { name: bams, type: \"bams\" },\n { name: genome_fasta, type: \"contigs\" },\n { name: fasta_index, type: \"fasta_index\" },\n { name: sequence_dict, type: \"sequence_dict\" }\n ],\n outputs: [\n { name: vcf, type: \"vcf\", file: \"{sample}_variants.vcf.gz\", description: \"Variants file\" },\n { name: stats, type: \"txt\", file: \"{sample}_vcf_stats.txt\", description: \"VCF stats\" }\n ],\n options:\n [\n {\n name: gatk3_haplotype_caller_threads,\n type: numeric,\n value: 4,\n min: 1,\n max: NA,\n step: 1,\n label: \"Number of threads to use\",\n },\n {\n name: gatk3_haplotype_caller_genome_fasta,\n type: input_file,\n value: \"\",\n label: \"Path to reference genome fasta file\",\n },\n ],\n },\n ],\n install: {\n # samtools: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/samtools\/samtools\/releases\/download\/1.9\/samtools-1.9.tar.bz2\",\n # \"tar -xvjf samtools-1.9.tar.bz2\",\n # \"cd samtools-1.9\",\n # \".\/configure && make\",\n # \"cd ..\",\n # \"mv samtools-1.9\/samtools bin\/samtools\",\n # \"rm -r samtools-1.9 samtools-1.9.tar.bz2\",\n # ],\n #gatk: [\n # \"cd \/opt\/biotools\",\n # \"wget https:\/\/github.com\/broadinstitute\/gatk\/releases\/download\/4.1.1.0\/gatk-4.1.1.0.zip\",\n # \"unzip gatk-4.1.1.0.zip\",\n # \"cd bin\",\n # \"ln -s \/opt\/biotools\/gatk-4.1.1.0\/gatk gatk\",\n # ],\n # gatk3: [\"#needs Java 1.8 !\",\n # \"cd \/opt\/biotools\",\n # \"wget -O GenomeAnalysisTK-3.6-0.tar.bz2 'https:\/\/storage.googleapis.com\/gatk-software\/package-archive\/gatk\/GenomeAnalysisTK-3.6-0-g89b7209.tar.bz2'\",\n # \"mkdir gatk3\",\n # \"tar -C gatk3 -xjf GenomeAnalysisTK-3.6-0.tar.bz2\",\n # \"rm GenomeAnalysisTK-3.6-0.tar.bz2\",\n # \"rm -r gatk3\/resources\"\n # ],\n # bcftools: [\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 # java8: [\n # \"apt -y update && apt install -y openjdk-8-jre\"\n # ]\n },\n citations: {\n gatk: [\n \"McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297\u20111303. https:\/\/doi.org\/10.1101\/gr.107524.110 \"\n ],\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 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" } ]