java -jar GenomeAnalysisTK.jar -T CombineVariants -R reference.fasta --variant input1.vcf --variant input2.vcf -o output.vcf -genotypeMergeOptions UNIQUIFY
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | VCF files to merge together | |
Optional Outputs | |||
--out  -o | stdout | File to which variants should be written | |
Optional Parameters | |||
--filteredrecordsmergetype  -filteredRecordsMergeType | KEEP_IF_ANY_UNFILTERED | Determines how we should handle records seen at the same site in the VCF, but with different FILTER fields | |
--genotypemergeoption  -genotypeMergeOptions | NA | Determines how we should merge genotype records for samples shared across the ROD files | |
--minimumN Â -minN | 1 | Minimum number of input files the site must be observed in to be included | |
--rod_priority_list  -priority | NA | Ordered list specifying priority for merging | |
--setKey | set | Key name for the set attribute | |
Optional Flags | |||
--assumeIdenticalSamples | false | Assume input VCFs have identical sample sets and disjoint calls | |
--excludeNonVariants  -env | false | Exclude sites where no variation is present after merging | |
--filteredAreUncalled | false | Treat filtered variants as uncalled | |
--mergeInfoWithMaxAC | false | Use the INFO content of the record with the highest AC | |
--minimalVCF | false | Emit a sites-only file | |
--printComplexMerges | false | Emit interesting sites requiring complex compatibility merging to file | |
--suppressCommandLineHeader | false | Do not output the command line to the header |