QuickStart

QuickStart

The core utility and main purpose of that tool is to MERGE VCFs information into one VCF without losing any data from the input vcfs vcfMerger2 can merge from 2 to N VCFs files.

###The simplest way for running vcfMerger2

The easiest way to use vcfMerger2 is:

1. to call on the vcfMerger2.py script in bin directory (normally in your PATH; ( See Installation )
2. to use somatic RAW VCFs from different variant caller as inputs

Inputs are RAW VCFs

Example_1

vcfMerger2.py  
-d ${DIRTEMP}  
-g ${REF_GENOME_FASTA} 
--dict ${REF_GENOME_DICT} 
--toolnames "tool1|tool2|tool3" 
--vcfs "tool1.raw.vcf|tool2.raw.vcf|tool3.raw.vcf" 
--prep-outfilenames "tool1.prepped.vcf|tool2.prepped.vcf|tool3.prepped.vcf"
--normal-sname NORMAL_SAMPLENAME  
--tumor-sname TUMOR_SAMPLENAME 
-o final_merged.vcf 

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Quick details about the options used above:
-d : Directory where the temporary files will be written ; final merged file will be writen in current directory unless relative of full path provided.
-g : Reference Genome in FASTA format
--dict: Dictionanry file for the Reference Genome given with -g
--toolnames : ordered piped list of somatic variant caller toolnames; To see the list of tool compatible with vcfMerger2, click here
--vcfs : ordered piped list of RAW VCFs from compatible somatic variant callers ; The order of the files in the list is important and must match the order of the toolnames given using --toolnames
--prep-outfilenames : ordered piped list of Intermediate names for the vcfMerger2-prepped VCFs. Order MUST match order given with --toolnames
--normal-sname : Name of the Constitutional Sample as defined in at least one of the given Somatic RAW VCF
--tumor-sname : Name of the Tumor Sample as defined in at least one of the given Somatic RAW VCF
-o : Name of the Final Merged VCF

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Help and Options

To get the full list of options of vcfMerger2, run:

vcfMerger2.py --help or python3 vcfMerger2.py --help
or
python3 ${DIR_INSTALL_VCF_MERGER2}/bin/vcfMerger2.py --help

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