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vcfMerger2 is a tool for merging from 2 to N vcfMerger2-specs somatic vcf files.
The merging process is the CORE of vcfMerger2 tool.
vcfMerger2 takes unprocessed or raw VCFs from different somatic variant callers and merge them losslessly.
This is the CORE functionnality of the vcfMerger2 tool: Merging N vcfs from somatic variant callers.
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
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
See OptionsAndArguments for more details about the options and inputs
Beside Merging, vcfMerger2 tool provides additional features:
- preparing VCFs to get vcfMerger2-prepped VCFs
- option to create venn diagrams or upset plots for the input VCFs
- options to filter VCFs [advanced users]
- merging Germline VCFs [feature under development]
For more details on the additional features, click here
vcfMerger2 is under MIT licence.
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