{ "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_VCF Pipeline:\n\nGVC_VCF is a pipeline developed at Genowis for germline and somatic mutation(snv, indel, sv) in next generation sequencing data.\n\nBasic Command Line Parameters Options:\n\n\tPositional Arguments:\n\t\tinput_json: The json file stores names and paths of both normal and tumor samples. \n\t\t\t\teg: {\"N\": [\"/disk/N.sort.dup.bam\"], \"T\": [\"/disk/T.sort.dup.bam\"]}\n\t\treference: The reference fasta file.\n\t\toutpath: The output folder.\n\tOptional Arguments:\n\t\t-h: Print help messages.\n\t\t--dbsnp: The Single Nucleotide Polymorphism Database(dbSNP) file has three columns(chr, position, rsID), Values on each line of the file are separated by tab.\n\t\t--bed: The WES file need to provide bed region, The bed region has at least three columns(chr,start,end), Values on each line of the file are separated by tab.\n\t\t--gvc_lib: The library folder has configuration file.\n\t\t\tThe docker volume file needs to be modified. A dictionary to configure volumes mounted inside the container. The key is either the host path or a volume name, and the value is a dictionary with the keys: \n\t\t\t\t\tbind: The path to mount the volume inside the container(the host path needs same with the container path).\n\t\t\t\t\tmode: rw to mount the volume read/write.\n\t\t\t\t\teg: {\"/disk\": {\"bind\": \"/disk\",\"mode\": \"rw\"}}\n\t\t--strategy: choose WES or WGS.\n\t\t--mutantType: Getting Germline mutation or Somatic mutaion.\n\t\t--sample_name: The Sample name.\n\nNote: the pipeline was writed by toil, so when running the programe, you need to provide jobStore(one dir name, eg: first_gvc_run or /home/first_gvc_run). 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