Compute the most likely genotype combination and phasing for trios and parent/child pairs
java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -R reference.fasta -V input.vcf -ped input.ped -o output.vcf
Argument name(s) | Default value | Summary | |
---|---|---|---|
Required Inputs | |||
--variant  -V | NA | Input VCF file | |
Optional Outputs | |||
--out  -o | stdout | An output file created by the walker. Will overwrite contents if file exists | |
Optional Parameters | |||
--DeNovoPrior  -prior | 1.0E-8 | Prior for de novo mutations. Default: 1e-8 | |
--MendelianViolationsFile  -mvf | NA | File to output the mendelian violation details. | |
Optional Flags | |||
--FatherAlleleFirst  -fatherAlleleFirst | false | Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father. |