java -jar GenomeAnalysisTK.jar -T RandomlySplitVariants -R reference.fasta -V input.vcf -o1 output_1.vcf -o2 output_2.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Outputs | |||
--out1 Â -o1 | stdout | File #1 to which variants should be written | |
--out2 Â -o2 | NA | File #2 to which variants should be written | |
Optional Parameters | |||
--fractionToOut1 Â -fraction | 0.5 | Fraction of records to be placed in out1 (must be 0 >= fraction | |
--numOfOutputVCFFiles  -N | -1 | number of output VCF files. Only works with SplitToMany = true | |
--prefixForAllOutputFileNames  -baseOutputName | NA | the name of the output VCF file will be: | |
Optional Flags | |||
--splitToManyFiles  -splitToMany | false | split (with uniform distribution) to more than 2 files. numOfFiles and baseOutputName parameters are required |