{"id":6304,"projects":[69],"description":"PCAWG MuSE variant calling workflow is developed by MD Anderson Cancer Center\n(http://bioinformatics.mdanderson.org/main/MuSE), it consists of software component calling structural\nvariants using uniformly aligned tumor / normal WGS sequences. The workflow has been dockerized and\npackaged using CWL workflow language, the source code is available on GitHub\nat: https://github.com/ICGC-TCGA-PanCancer/pcawg-muse.\n\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\nsettings.\n\n#### Hardware requirement (assuming 30X 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. For improved calling result we pre-process the aligned BAMs using PCAWG GATK\nCo-cleaning workflow, see [here](https://dockstore.org/workflows/ICGC-TCGA-PanCancer/pcawg-gatk-cocleaning)\nfor more information how to run it.\n\nHere we assume aligned pre-processed BAMs are *tumor_sample.bam* and *normal_sample.bam*,\nand are under *bams* subfolder.\n\n#### Reference data files\n\nThe workflow also uses two reference files as input, both can be downloaded from the ICGC Data Portal:\n- reference genome sequence *genome.fa.gz* under https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-bwa-mem\n- known dbSNP entries *dbsnp_132_b37.leftAligned.vcf.gz* under https://dcc.icgc.org/releases/PCAWG/reference_data/pcawg-muse\n\nWe assume the reference files are under *reference* subfolder.\n\n#### Job JSON file for CWL\n\nFinally, we need to prepare a JSON file with input, reference files specified. Please replace the\n*tumor* and *normal* parameters with your real BAM files.\n\nName the JSON file: *pcawg-muse-variant-caller.job.json*\n```\n{\n    \"mode\": \"wgs\",\n    \"tumor\": {\n         \"class\": \"File\",\n         \"location\": \"bams/tumor_sample.bam\"\n     },\n     \"normal\": {\n        \"class\": \"File\",\n        \"location\": \"bams/normal_sample.bam\"\n    },\n    \"reference\": {\n        \"class\": \"File\",\n        \"location\": \"reference/genome.fa.gz\"\n    },\n    \"known\": {\n        \"class\": \"File\",\n        \"location\": \"reference/dbsnp_132_b37.leftAligned.vcf.gz\"\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-muse-variant-caller.cwl \"https://raw.githubusercontent.com/ICGC-TCGA-PanCancer/pcawg-muse/0.1.2/muse.cwl\"\n```\n\n- Run `cwltool` to execute the workflow\n```\nnohup cwltool --debug --non-strict pcawg-muse-variant-caller.cwl pcawg-muse-variant-caller.job.json > pcawg-muse-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-muse","url":"https://dockstore.org/api/api/ga4gh/v2/tools/quay.io%2Fpancancer%2Fpcawg-muse","authors":[1],"rubrics":[25]}