Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta --variant input1.vcf --variant input2.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAVCF files to merge together
Optional Outputs
--out
 -o
stdoutFile to which variants should be written
Optional Parameters
--filteredrecordsmergetype
 -filteredRecordsMergeType
KEEP_IF_ANY_UNFILTEREDDetermines how we should handle records seen at the same site in the VCF, but with different FILTER fields
--genotypemergeoption
 -genotypeMergeOptions
NADetermines how we should merge genotype records for samples shared across the ROD files
--minimumN
 -minN
1Minimum number of input files the site must be observed in to be included
--rod_priority_list
 -priority
NAOrdered list specifying priority for merging
--setKey
setKey name for the set attribute
Optional Flags
--assumeIdenticalSamples
falseAssume input VCFs have identical sample sets and disjoint calls
--excludeNonVariants
 -env
falseExclude sites where no variation is present after merging
--filteredAreUncalled
falseTreat filtered variants as uncalled
--mergeInfoWithMaxAC
falseUse the INFO content of the record with the highest AC
--minimalVCF
falseEmit a sites-only file
--printComplexMerges
falseEmit interesting sites requiring complex compatibility merging to file
--suppressCommandLineHeader
falseDo not output the command line to the header


Share your experience or ask a question