gvc4bam 1.0.10

GVC_VCF Pipeline:

GVC_VCF is a pipeline developed at Genowis for germline and somatic mutation(snv, indel, sv) in next generation sequencing data.

Basic Command Line Parameters Options:

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.

Note: 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). A job store holds persistent information about the jobs and files in a workflow. Eg： 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

demo: 192.168.75.200 /disk/chenfs/gvc_vcf_pipeline/demo, the demo taked 4 minutes. 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