gvc4bam是基因组智慧公司开发的数据处理管道。gvc4fastq从bam文件中检测生殖系和体细胞突变（snv，indel，sv）。
gvc4bam的Python项目详细描述
全球价值链vcf管道：
gvc-vcf是genowis为下一代测序数据中的生殖系和体细胞突变（snv，indel，sv）开发的一个管道。
基本命令行参数选项：
Positional Arguments:
input_json: The json file stores names and paths of both normal and tumor samples.
eg: {"N": ["/disk/N.sort.dup.bam"], "T": ["/disk/T.sort.dup.bam"]}
reference: The reference fasta file.
outpath: The output folder.
Optional Arguments:
-h: Print help messages.
--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.
--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.
--gvc_lib: The library folder has configuration file.
The 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:
bind: The path to mount the volume inside the container(the host path needs same with the container path).
mode: rw to mount the volume read/write.
eg: {"/disk": {"bind": "/disk","mode": "rw"}}
--strategy: choose WES or WGS.
--mutantType: Getting Germline mutation or Somatic mutaion.
--sample_name: The Sample name.
注意：管道是由toil编写的，因此在运行程序时，需要提供jobstore（一个目录名，例如：first-gvc-run或/home/first-gvc-run）。作业存储保存有关工作流中作业和文件的持久信息。 如： python gvc_vcf_pipeline.py first_gvc_run/disk/gvc_vcf_pipeline/bam.json/disk/db/ref/human.fa/disk/gvc_vcf_pipeline/outpath/--dbsnp/disk/db/dbsnp/dbsnp_frequency--bed/disk/data/no_ref.ccd--gvc_lib/disk/gvc_vcf_pipeline/gvc_lib/--muntattype sonal--muntattype germline--sample_name test_data--strategy wes
演示：192.168.75.200
/磁盘/chenfs/gvc_vcf_pipeline/演示，演示需要4分钟。
python/disk/chenfs/gvc vcf管道/src/gvc vcf管道.py
第一次全球价值链运行
/磁盘/chenfs/gvc\u vcf\u pipeline/demo/demo.json
/磁盘/db/ref/human.fa
/磁盘/chenfs/gvc/vcf管道/demo/test/
--dbsnp/磁盘/db/dbsnp/dbsnp_频率
--床/磁盘/chenfs/gvc_vcf_pipeline/demo/demo.bed
--gvc-lib/磁盘/chenfs/gvc-vcf-u管道/gvc-lib/
--突变体体细胞——突变体生殖系——策略WES
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