Category

Genome Variant Analysis


Usage

java -jar GenomeAnalysisTK.jar -T PhaseByTransmission -R reference.fasta -V input.vcf -ped input.ped -o output.vcf


Manual

Argument name(s)Default valueSummary
Required Inputs
--variant
 -V
NAInput VCF file
Optional Outputs
--out
 -o
stdoutAn output file created by the walker. Will overwrite contents if file exists
Optional Parameters
--DeNovoPrior
 -prior
1.0E-8Prior for de novo mutations. Default: 1e-8
--MendelianViolationsFile
 -mvf
NAFile to output the mendelian violation details.
Optional Flags
--FatherAlleleFirst
 -fatherAlleleFirst
falseOuputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.


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