Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -R reference.fasta -T VariantsToTable -V file.vcf -F CHROM -F POS -F ID -F QUAL -F AC -o results.table


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Outputs
--out
 -o
stdoutFile to which results should be written
Optional Parameters
--fields
 -F
[]The name of each field to capture for output in the table
--genotypeFields
 -GF
[]The name of each genotype field to capture for output in the table
--maxRecords
 -M
-1If provided, we will emit at most maxRecord records to the table
Optional Flags
--splitMultiAllelic
 -SMA
falseIf provided, we will split multi-allelic records into multiple lines of output
Advanced Flags
--allowMissingData
 -AMD
falseIf provided, we will not require every record to contain every field
--moltenize
falseIf provided, we will produce molten output
--showFiltered
 -raw
falseIf provided, field values from filtered records will be included in the output


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