Extract specific fields from a VCF file to a tab-delimited table
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
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Outputs | |||
--out  -o | stdout | File 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 | -1 | If provided, we will emit at most maxRecord records to the table | |
Optional Flags | |||
--splitMultiAllelic  -SMA | false | If provided, we will split multi-allelic records into multiple lines of output | |
Advanced Flags | |||
--allowMissingData  -AMD | false | If provided, we will not require every record to contain every field | |
--moltenize | false | If provided, we will produce molten output | |
--showFiltered  -raw | false | If provided, field values from filtered records will be included in the output |