Genome Variant Analysis


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


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

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