{
    "info": {
        "author": "LongHui.Yin",
        "author_email": "dragonfly.yin@genowis.com",
        "bugtrack_url": null,
        "classifiers": [
            "License :: Free For Educational Use",
            "Programming Language :: Python :: 2.7"
        ],
        "description": "## GVC\u57fa\u56e0\u7ec4\u7a81\u53d8\u63a2\u6d4b\u5957\u4ef6\u4f7f\u7528\u8bf4\u660e\n\nGVC\uff08Genomic Variant Caller\uff09\u57fa\u56e0\u7ec4\u7a81\u53d8\u63a2\u6d4b\u5957\u4ef6\u662f\u7531\u5fd7\u8bfa\u7ef4\u601d\u81ea\u4e3b\u7814\u53d1\u7684\u4e00\u6b3e\u4eba\u5de5\u667a\u80fd\u53d8\u5f02\u63a2\u6d4b\u52a0\u901f\u8f6f\u4ef6\u3002\u5229\u7528\u4e8c\u4ee3\u6d4b\u5e8f\u6570\u636e\u53ef\u4ee5\u5bf9\u9057\u4f20\u6027\u80da\u7cfb\uff08Germline\uff09\u548c\u80bf\u7624\u4f53\u7ec6\u80de\uff08Somatic\uff09\u53d8\u5f02\u8fdb\u884c\u68c0\u6d4b\u5206\u6790\uff0c\u652f\u6301FASTQ\u6216\u8005BAM\u7684\u6807\u51c6\u6587\u4ef6\u8f93\u5165\u683c\u5f0f\uff0c\u53ef\u5bf9\u591a\u79cd\u53d8\u5f02\u7c7b\u578b\uff08SNP\u3001SNV\u3001sINDEL\u3001SV\u548cCNV\uff09\u4e00\u6b21\u6027\u540c\u65f6\u63a2\u6d4b\uff0c\u8f6f\u4ef6\u7cbe\u51c6\u5ea6\u8d85\u8fc7\u4e3b\u6d41\u516c\u8ba4\u7684\u7b97\u6cd5\u8f6f\u4ef6\uff0c\u7a81\u53d8\u63a2\u6d4b\u7684\u901f\u5ea6\u548c\u8fd0\u884c\u6548\u7387\u5e73\u5747\u63d0\u534720\u500d\uff0c\u5305\u542b\u6bd4\u5bf9\u7684\u6574\u4f53\u6d41\u7a0b\u6548\u7387\u63d0\u53475\u500d\u3002\u76ee\u524d\u7248\u672c\u652f\u6301WGS\u3001WES\u548cPanel\u7684\u6d4b\u5e8f\u7c7b\u578b\uff0c\u80bf\u7624\u53d8\u5f02\u63a2\u6d4b\u5fc5\u987b\u4e3a\u542b\u5bf9\u7167\u7684\u7ec4\u7ec7\u6837\u54c1\u6d4b\u5e8f\uff0c\u80bf\u7624\u6837\u54c1\u7684\u8986\u76d6\u6df1\u5ea6\u5efa\u8bae\u5728100X-1000X\u4e4b\u95f4\u3002\u5ba2\u6237\u5982\u6709\u5bf9\u751f\u4ea7\u6570\u636e\u7684\u6a21\u578b\u5b9a\u5236\u3001\u7cbe\u5ea6\u63d0\u5347\u6216\u5176\u4ed6\u6d4b\u5e8f\u5e94\u7528\u573a\u666f\u7684\u9700\u6c42\u8bf7\u76f4\u63a5\u8054\u7cfb\u6211\u4eec\u7684\u6280\u672f\u652f\u6301\u4eba\u5458\u3002\n\n## \u4e00\u3001\u90e8\u7f72\u73af\u5883\u8981\u6c42\n\n```\nLinux\u7cfb\u7edf\u5185\u6838\u7248\u672c\u9ad8\u4e8e3.10\n\u670d\u52a1\u5668\u5185\u5b58\u5927\u4e8e16G\n\u670d\u52a1\u5668\u7ebf\u7a0b\u6570\u5927\u4e8e10\n```\n\n## \u4e8c\u3001\u5b89\u88c5\u8bf4\u660e\n\n### 1. \u5b89\u88c5\u5fc5\u987b\u8f6f\u4ef6\u5305\n\n```\nyum install -y epel-release\nyum -y install docker python python-devel python-pip gcc zlib-devel bzip2-devel xz-devel \nsystemctl start docker\n\n```\n\n*\u6ce8\u610f\uff1a\u7528\u6237\u5fc5\u987b\u53ef\u4ee5\u8fd0\u884cdocker\u547d\u4ee4\u624d\u80fd\u8fd0\u884cGVC\uff0c\u5982\u679c\u9700\u8981\u8ba9\u67d0\u4e2a\u666e\u901a\u7528\u6237\uff08\u4f8b\u5982 USER_NAME\uff09\u5177\u6709\u6b64\u6743\u9650\uff0c\u53ef\u4ee5\u4f7f\u7528\u5982\u4e0b\u547d\u4ee4. \u53c2\u8003\uff1ahttps://docs.docker.com/install/linux/linux-postinstall/*\n\n```\ngroupadd docker\ngpasswd -a USER_NAME docker\nsystemctl restart docker\n#if you are currently login as USER_NAME\n#please logout and login again\n```\n\n### 2. \u83b7\u53d6GVC\u6240\u9700Docker\u955c\u50cf\n\n*\u6ce8\u610f\uff1a\u5982\u679c\u672c\u5730\u4e0b\u8f7ddocker hub\u91cc\u7684\u955c\u50cf\u8fc7\u6162\uff0c\u53ef\u4ee5\u8003\u8651\u5728/etc/docker/daemon.json\u91cc\u589e\u52a0\u5982\u4e0b\u914d\u7f6e\u6765\u52a0\u901f*\n\n```\n\"registry-mirrors\": \n\t[\"https://registry.docker-cn.com\",\n\t\"http://hub-mirror.c.163.com\",\n\t\"https://docker.mirrors.ustc.edu.cn\"]\n```\n\n\u6700\u7ec8\u7684/etc/docker/daemon.json\u5185\u5bb9\u53ef\u4ee5\u662f\u8fd9\u6837\uff1a\n\n```\n{\n  \"live-restore\": true,\n  \"registry-mirrors\": \n  \t[\"https://registry.docker-cn.com\",\n  \t\"http://hub-mirror.c.163.com\",\n  \t\"https://docker.mirrors.ustc.edu.cn\"]\n}\n```\n\n\u9700\u8981\u91cd\u542fdocker\u670d\u52a1\u6765\u8ba9\u65b0\u914d\u7f6e\u751f\u6548\n\n```\nsudo systemctl restart docker\n```\n\n### 3.\u5b89\u88c5python\u76f8\u5173\u7ec4\u4ef6\n\n#### \u5b89\u88c5python\uff0c\u4ee5\u53ca\u72ec\u7acbpython\u73af\u5883\n\n```\n#Please note, gvc4fastq can only run with Python 2.7\n#Consider of using virtualenv to create a sperate env\n\n##\u5982\u679c\u60f3\u542f\u7528\u4e00\u4e2a\u540d\u4e3avenv\u7684\u72ec\u7acbpython\u8fd0\u884c\u73af\u5883\uff0c\n##\u907f\u514d\u4e0e\u5f53\u524dpython\u73af\u5883\u4e92\u76f8\u5e72\u6270\uff0c\u53ef\u4ee5\u5b89\u88c5virtualenv\n#pip install virtualenv\n#virtualenv ~/venv       \n#source ~/venv/bin/activate   #\u8fdb\u5165\u8be5\u72ec\u7acb\u7684python\u73af\u5883\n\npip install gvc4fastq\n\n```\n\n### 4.\u83b7\u53d6\u6a21\u578b\u6587\u4ef6\u5305\u548cdocker\u5305\n\nGVC\u4f7f\u7528\u673a\u5668\u5b66\u4e60\u7b97\u6cd5\uff0c\u4f7f\u7528GVC\u5fc5\u987b\u914d\u5408\u4f7f\u7528\u76f8\u5e94\u7684\u6a21\u578b\u6587\u4ef6\u3002\u6700\u65b0\u7248\u672c\u6a21\u578b\u6587\u4ef6\u53ef\u4ee5\u8fd9\u6837\u83b7\u53d6:\n\n```\nwget https://gvc.obs.cn-north-1.myhuaweicloud.com/gvc_lib.tar.gz\ntar zxf gvc_lib.tar.gz\n```\n\n\u66f4\u65b0\u5e93\u6587\u4ef6\u4e2ddocker\u5305\u7248\u672c\u4fe1\u606f\u5e76\u83b7\u53d6\u6700\u65b0docker\u5305\n\n```\nwget https://gvc.obs.cn-north-1.myhuaweicloud.com/version.json -O gvc_lib/version.json\ncat gvc_lib/version.json |awk '{print $2}'|awk -F '\"' '{print $2}'|xargs -I % docker pull %\n```\n\n### 5.\u5b89\u88c5license\n\n#### \u81ea\u52a8\u83b7\u53d6\u8bd5\u7528license\n\n\u8bf7\u767b\u5f55 https://gvc.0cancer.cn/application \u586b\u5199\u8868\u5355\uff0c\u6309\u7167\u90ae\u4ef6\u6307\u5f15\u64cd\u4f5c\u3002\n\n#### \u6b63\u5f0f\u91c7\u8d2d\n\n\u9996\u5148\u83b7\u53d6\u673a\u5668\u7801\n\n\u64cd\u4f5c\u7cfb\u7edf\u88c5\u597dDocker\u540e\uff0c\u53ef\u76f4\u63a5\u8fd0\u884c\u5982\u4e0b\u547d\u4ee4\u6765\u83b7\u53d6\u673a\u5668\u7801\n\n```\ndocker run --network=host genowisgvc/id:latest\n```\n\n\u4f8b\u5982\uff1a\n\n```\n$ docker run --network=host genowisgvc/id:latest\nIVDA-BBAA-LHep-zQAA:uU9c0qCsUnYKLNnEgagvKw==\n```\n\n\u8054\u7cfb\u5fd7\u8bfa\u7ef4\u601d\u53d6\u5f97license\u6587\u4ef6\n\n\u53d6\u5f97\u6240\u6709\u9700\u8981\u5b89\u88c5GVC\u7684\u670d\u52a1\u5668\u7684\u673a\u5668\u7801\uff0c\u53d1\u9001\u7ed9\u6211\u4eec\u5ba2\u6237\u652f\u6301\u4fe1\u7bb1 support@genowis.com\uff0c\u6211\u4eec\u5c06\u4f1a\u7ed9\u4f60\u4eec\u53d1\u9001\u4e00\u4e2alicense.txt\u6587\u4ef6\u548cgvc.lic\u6587\u4ef6\uff0c\u5c06\u8fd9\u4e24\u4e2a\u6587\u4ef6\u653e\u5165gvc_lib\u76ee\u5f55\u4e0b\u5373\u53ef\u5b8c\u6210\u6fc0\u6d3b\u3002\n\n\n## \u4e09\u3001\u4f7f\u7528\u8bf4\u660e\n\n### \u4f7f\u7528bam_vcf\u6d41\u7a0b\n\n```\nbam_vcf.py:\n\nusage: bam_vcf.py [options] input_json reference outpath\n\n\u5fc5\u8981\u53c2\u6570\n\n    input_json:# json\u6587\u4ef6\u4e2d\u914d\u7f6e\u4e86Normal BAM \u548c Tumor BAM \u7684\u8def\u5f84\u4fe1\u606f\n               # \u8bf7\u4f7f\u7528bwa-mem\u6bd4\u5bf9\u751f\u6210\u7684\u6392\u5e8f\u540e\u7684bam\uff0c\u6682\u4e0d\u652f\u6301\u5176\u4ed6\u6bd4\u5bf9\u8f6f\u4ef6\u3002\n               # \u80bf\u7624\u4f53\u7ec6\u80de\u53d8\u5f02\uff0cjson\u6587\u4ef6\u683c\u5f0f: \n               # {\"N\": [\"/path/N.sort.bam\"], \"T\": [\"/path/T.sort.bam\"]}\n               # \u9057\u4f20\u6027\u80da\u7cfb\u53d8\u5f02\uff0cjson\u6587\u4ef6\u683c\u5f0f\n               # {\"T\": [\"/path/sample.sort.bam\"] }\n\n\n    reference: \n             # \u53c2\u8003\u5e8f\u5217\uff0c\u4f8b\u5982 /disk/human.fa\n              # \u6ce8\u610f\u6b64\u8def\u5f84\u9700\u8981\u5305\u542b\u53c2\u8003\u5e8f\u5217\u7d22\u5f15\u6587\u4ef6 /disk/human.fa.fai\n\n    outpath\uff1a\n             # \u8f93\u51fa\u8def\u5f84\u53c2\u6570\uff0c\u4f8b\u5982 /disk/output\n\n    --gvc_lib: \n             # \u5e93\u6587\u4ef6\u548c\u914d\u7f6e\u6587\u4ef6\u8def\u5f84\n\n    --strategy: \n             # \u6d4b\u5e8f\u7c7b\u578b\u9009\u62e9\uff0c\u652f\u6301WGS, WES\u548cPanel\n\n    --dbsnp:   \n             # dbSNP\u5e93\uff08The Single Nucleotide Polymorphism Database\uff09\n             # \u5305\u542b\u4e09\u5217\uff0c\u5206\u522b\u662f Chr, Position, rsID \uff0c\u5217\u4e4b\u95f4\u901a\u8fc7tab\u9694\u5f00\n\n    --bed:     \n             # bed\u6587\u4ef6\u5305\u542b\u4e09\u5217\uff0c\u5206\u522b\u662fchr, start, end, \u901a\u8fc7tab\u9694\n\n    --sample_name:   \n             # \u6837\u54c1\u540d\n    --mutantType :   \n             # somatic\uff08\u80bf\u7624\u4f53\u7ec6\u80de\u53d8\u5f02\uff09 \uff0c germline \uff08\u9057\u4f20\u6027\u80da\u7cfb\u53d8\u5f02\uff09 \u53ef\u540c\u65f6\u9009\u62e9\u4e24\u8005\n\n\u53ef\u9009\u53c2\u6570\uff1a\t\n    --segmentSize:  \n              # \u9ed8\u8ba4\u5355\u7ebf\u7a0b\u8fd0\u884c\uff0c\u6b64\u53c2\u6570\u5207\u5206bam\u52a0\u901f\uff0c\n\t      # \u598220000000 \uff0c\u5bf9bed\u533a\u57df\u8fdb\u884c20M\u5927\u5c0f\u5207\u5206\n    --maxCores: \n              #\u6307\u5b9a\u4f7f\u7528\u7684\u6700\u5927\u7ebf\u7a0b\u6570\n    --maxMemory\uff1a\n              #\u6307\u5b9a\u4f7f\u7528\u7684\u6700\u5927\u5185\u5b58\u6570\n    --CNV\uff1a\n              #\u8f93\u51faCNV\u7ed3\u679c\n    --SV\uff1a\n              #\u8f93\u51faSV\u7ed3\u679c\n```\n\n### \u793a\u4f8b\uff1a\n\n```\n$ bam_vcf.py \\\n\t/absolute/path/to/demo/demo.json \\    # input_json\n\t/absolute/path/to/demo/human.fa \\     # gvc_lib path\n\t/absolute/path/to/demo/test \\         # output path\n\t--dbsnp /absolute/path/to/demo/dbsnp_138-1000G-snp \\\n\t--bed /absolute/path/to/demo/demo.bed \\\n\t--gvc_lib /absolute/path/to/gvc_lib \\ \n\t--strategy WES  \\\n\t--segmentSize 20000000 \\\n\t--sample_name demo_sample_name \\\n\t--mutantType  somatic \n\n\n```\n\n### \u4f7f\u7528fastq_vcf\u6d41\u7a0b\n\n```\nfastq_vcf.py:\n\nusage: fastq_vcf.py [options] input_json reference outpath\n\n\u5fc5\u8981\u53c2\u6570\n\n    input_json:# json\u6587\u4ef6\u4e2d\u914d\u7f6e\u4e86Normal BAM \u548c Tumor BAM \u7684\u8def\u5f84\u4fe1\u606f\n              # \u8bf7\u4f7f\u7528bwa-mem\u6bd4\u5bf9\u751f\u6210\u7684\u6392\u5e8f\u540e\u7684bam\uff0c\u6682\u4e0d\u652f\u6301\u5176\u4ed6\u6bd4\u5bf9\u8f6f\u4ef6\u3002\n              # \u80bf\u7624\u4f53\u7ec6\u80de\u53d8\u5f02\uff0cjson\u6587\u4ef6\u683c\u5f0f\uff1a\n              # {\n              #\t\"N\": { \"R1\": [\"/disk/N_1.fastq.gz\"], \"R2\": [\"/disk/N_2.fastq.gz\"] },\n              #\t\"T\": { \"R1\": [\"/disk/T_1.fastq.gz\"], \"R2\": [\"/disk/T_2.fastq.gz\"] }\n              # }\n              # \u9057\u4f20\u6027\u80da\u7cfb\u53d8\u5f02\u63a2\u6d4b\uff0cjson\u6587\u4ef6\u683c\u5f0f\uff1a\n              # {\n              #   \"T\": {\"R1\":[\"/disk/demo_1.fastq.gz\"],\"R2\":[\"/disk/demo_2.fastq.gz\"]}\n              # }\n\n\n  reference: \n              # \u53c2\u8003\u5e8f\u5217\uff0c\u4f8b\u5982 /disk/human.fa\n              # \u6ce8\u610f\u6b64\u8def\u5f84\u9700\u8981\u5305\u542b\u53c2\u8003\u5e8f\u5217\u7d22\u5f15\u6587\u4ef6 /disk/human.fa.fai\n\n    outpath\uff1a \n              # \u8f93\u51fa\u8def\u5f84\u53c2\u6570\uff0c\u4f8b\u5982 /disk/output\n\n    --gvc_lib: \n             # \u5e93\u6587\u4ef6\u548c\u914d\u7f6e\u6587\u4ef6\u8def\u5f84\n\n    --strategy: \n              # \u6d4b\u5e8f\u7c7b\u578b\u9009\u62e9\uff0c\u652f\u6301WGS, WES\u548cPanel\n\n    --dbsnp: \n              # dbSNP\u5e93\uff08The Single Nucleotide Polymorphism Database\uff09\n              # \u5305\u542b\u4e09\u5217\uff0c\u5206\u522b\u662f Chr, Position, rsID \uff0c\u5217\u4e4b\u95f4\u901a\u8fc7tab\u9694\u5f00\n\n    --bed:     \n              # bed\u6587\u4ef6\u5305\u542b\u4e09\u5217\uff0c\u5206\u522b\u662fchr, start, end, \u901a\u8fc7tab\u9694\n\n    --sample_name:  \n              # \u6837\u54c1\u540d\n    --mutantType :   \n              # somatic\uff08\u80bf\u7624\u4f53\u7ec6\u80de\u53d8\u5f02\uff09 \uff0c germline \uff08\u9057\u4f20\u6027\u80da\u7cfb\u53d8\u5f02\uff09\u53ef\u540c\u65f6\u9009\u62e9\u4e24\u8005\n\n\u53ef\u9009\u53c2\u6570\uff1a\n    --segmentSize:  \n              # \u9ed8\u8ba4\u5355\u7ebf\u7a0b\u8fd0\u884c\uff0c\u6b64\u53c2\u6570\u5207\u5206bam\u52a0\u901f\uff0c\n              # \u598220000000 \uff0c\u5bf9bed\u533a\u57df\u8fdb\u884c20M\u5927\u5c0f\u5207\u5206\n    --maxCores: \n              #\u6307\u5b9a\u4f7f\u7528\u7684\u6700\u5927\u7ebf\u7a0b\u6570\n    --maxMemory\uff1a\n              #\u6307\u5b9a\u4f7f\u7528\u7684\u6700\u5927\u5185\u5b58\u6570\n    --CNV\uff1a\n              #\u8f93\u51faCNV\u7ed3\u679c\n    --SV\uff1a\n              #\u8f93\u51faSV\u7ed3\u679c\n```\n\n### \u793a\u4f8b\uff1a\n\n```\n$ fastq_vcf.py \\\n\t/absolute/path/to/demo/demo.json \\    # input_json\n\t/absolute/path/to/demo/human.fa \\     # gvc_lib path\n\t/absolute/path/to/demo/test \\         # output path\n\t--dbsnp /absolute/path/to/demo/dbsnp_138-1000G-snp \\\n\t--bed /absolute/path/to/demo/demo.bed \\\n\t--gvc_lib /absolute/path/to/gvc_lib \\\n\t--strategy WES  \\\n\t--segmentSize 20000000 \\\n\t--sample_name demo_sample_name \\\n    --mutantType  somatic\n```\n\n## \u56db\u3001\u6d4b\u8bd5\u5b9e\u4f8b\n\n\u7528\u6237\u53ef\u4ee5\u4e0b\u8f7d\u5e76\u6267\u884c\u4e00\u4e2a\u5c0f\u6d4b\u8bd5\u96c6\u6765\u9a8c\u8bc1\u5b89\u88c5\u662f\u5426\u6210\u529f\n\n```\n#get reference data\nwget --no-check-certificate https://gvc.obs.cn-north-1.myhuaweicloud.com/ref.tar.gz\ntar zxf ref.tar.gz\n\n#get test data set\nwget --no-check-certificate https://gvc.obs.cn-north-1.myhuaweicloud.com/test_set.tar.gz\ntar zxf test_set.tar.gz\n\n#run GVC\n\n#prepare the output folder\nmkdir /tmp/output\n\n#please use absolute path for all parameters\n# we need these information to run GVC:\n# path for fastq files\n# path to reference\n# output folder\n# dbSNP file\n# bed file\n# gvc_lib pathname\n# sample name\n# WGS, WES or Panel\n# Somatic or Germline\n# You can read the user 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