GVC4BAM 是由 Genome Wisdom Inc. 开发的数据处理管道。GVC4FASTQ 从 BAM 文件中检测种系和体细胞突变（SNV、InDel、SV）。
项目描述
GVC_VCF 管道：
GVC_VCF 是 Genowis 为下一代测序数据中的种系和体细胞突变（snv、indel、sv）开发的管道。
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：管道是辛苦写的，所以在运行程序时，需要提供jobStore（一个目录名，eg: first_gvc_run or /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。例如： 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/ --mutantType Somatic --mutantType Germline --sample_name test_data --strategy WES
演示：192.168.75.200 /disk/chenfs/gvc_vcf_pipeline/demo，演示耗时4分钟。python /disk/chenfs/gvc_vcf_pipeline/src/gvc_vcf_pipeline.py
first_gvc_run
/disk/chenfs/gvc_vcf_pipeline/demo/demo.json
/disk/db/ref/human.fa
/disk/chenfs/gvc_vcf_pipeline/demo/test/
--dbsnp /disk/db/dbsnp/dbsnp_frequency
--bed /disk/chenfs/gvc_vcf_pipeline/demo/demo.bed
--gvc_lib /disk/chenfs/gvc_vcf_pipeline/gvc_lib/
--mutantType Somatic --mutantType Germline --strategy WES
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