{"id":6292,"projects":[69],"description":"PCAWG Sanger variant calling workflow is developed by Wellcome Trust Sanger Institute\n(http://www.sanger.ac.uk/), it consists of software components calling somatic substitutions,\nindels and structural variants using uniformly aligned tumour / normal WGS sequences.\nThe workflow has been dockerized and packaged using CWL workflow language, the source code\nis available on GitHub at: https://github.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker.\n\n## Run the workflow with your own data\n\n### Prepare compute environment and install software packages\nThe workflow has been tested in Ubuntu 16.04 Linux environment with the following hardware and software settings.\n\n#### Hardware requirement (assuming X30 coverage whole genome sequence)\n- CPU core: 16\n- Memory: 64GB\n- Disk space: 1TB\n\n#### Software installation\n- Docker (1.12.6): follow instructions to install Docker https://docs.docker.com/engine/installation\n- CWL tool\n```\npip install cwltool==1.0.20170217172322\n```\n\n### Prepare input data\n#### Input aligned tumor / normal BAM files\n\nThe workflow uses a pair of aligned BAM files as input, one BAM for tumor, the other for normal,\nboth from the same donor. Here we assume file names are *tumor_sample.bam* and *normal_sample.bam*,\nand both files are under *bams* subfolder.\n\n#### Reference data files\n\nThe workflow also uses two precompiled reference files (*GRCh37d5_CGP_refBundle.tar.gz*,\n*GRCh37d5_battenberg.tar.gz*) as input, they can be downloaded from the\nICGC Data Portal under https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-sanger.\nWe assume the two reference files are downloaded and put under *reference* subfolder.\n\n#### Job JSON file for CWL\n\nFinally, we need to prepare a JSON file with input, reference and output files specified. Please replace\nthe *tumor* and *normal* parameters with your real BAM file names. Parameters for output are file name\nsuffixes, usually don't need to be changed.\n\nName the JSON file: *pcawg-sanger-variant-caller.job.json*\n```\n{\n  \"tumor\":\n  {\n    \"path\":\"bams/tumor_sample.bam\",\n    \"class\":\"File\"\n  },\n  \"normal\":\n  {\n    \"path\":\"bams/normal_sample.bam\",\n    \"class\":\"File\"\n  },\n  \"refFrom\":\n  {\n    \"path\":\"reference/GRCh37d5_CGP_refBundle.tar.gz\",\n    \"class\":\"File\"\n  },\n  \"bbFrom\":\n  {\n    \"path\":\"reference/GRCh37d5_battenberg.tar.gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_snv_mnv_tar_gz\":\n  {\n    \"path\":\"somatic_snv_mnv_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_cnv_tar_gz\":\n  {\n    \"path\":\"somatic_cnv_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_sv_tar_gz\":\n  {\n    \"path\":\"somatic_sv_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_indel_tar_gz\":\n  {\n    \"path\":\"somatic_indel_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_imputeCounts_tar_gz\":\n  {\n    \"path\":\"somatic_imputeCounts_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_genotype_tar_gz\":\n  {\n    \"path\":\"somatic_genotype_tar_gz\",\n    \"class\":\"File\"\n  },\n  \"somatic_verifyBamId_tar_gz\":\n  {\n    \"path\":\"somatic_verifyBamId_tar_gz\",\n    \"class\":\"File\"\n  }\n}\n```\n\n### Run the workflow\n#### Option 1: Run with CWL tool\n- Download CWL workflow definition file\n```\nwget -O pcawg-sanger-variant-caller.cwl \"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/CGP-Somatic-Docker/2.0.3/Dockstore.cwl\"\n```\n\n- Run `cwltool` to execute the workflow\n```\nnohup cwltool --debug --non-strict pcawg-sanger-variant-caller.cwl pcawg-sanger-variant-caller.job.json > pcawg-sanger-variant-caller.log 2>&1 &\n```\n\n#### Option 2: Run with the Dockstore CLI\nSee the *Launch with* section below for details.","image":"","tags":"","type":"","title":"pcawg-sanger-cgp-workflow","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fpancancer%2Fpcawg-sanger-cgp-workflow","authors":[1],"rubrics":[25]}