Computes the most likely genotype combination and phases trios and parent/child pairs
PhaseByTransmission is a GATK tool that 1) computes the most likely genotype combination and phases trios and parent/child pairs given their genotype likelihoods and a mutation prior and 2) phases all sites were parent/child transmission can be inferred unambiguously. It reports the genotype combination (and hence phasing) probability. Ambiguous sites are:
An VCF with genotypes recalibrated as most likely under the familial constraint and phased by descent where non ambiguous..
java -Xmx2g -jar GenomeAnalysisTK.jar \ -R ref.fasta \ -T PhaseByTransmission \ -V input.vcf \ -ped input.ped \ -o output.vcf
These Read Filters are automatically applied to the data by the Engine before processing by PhaseByTransmission.
This tool overrides the engine's default downsampling settings.
The arguments described in the entries below can be supplied to this tool to modify its behavior. For example, the -L argument directs the GATK engine restricts processing to specific genomic intervals (this is an Engine capability and is therefore available to all GATK walkers).
This table summarizes the command-line arguments that are specific to this tool. For details, see the list further down below the table.
|--variant||RodBinding[VariantContext]||NA||Input VCF file|
|--out||VariantContextWriter||stdout||An output file created by the walker. Will overwrite contents if file exists|
|--DeNovoPrior||double||1.0E-8||Prior for de novo mutations. Default: 1e-8|
|--MendelianViolationsFile||PrintStream||NA||File to output the mendelian violation details.|
|--FatherAlleleFirst||boolean||false||Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.|
Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.
Prior for de novo mutations. Default: 1e-8.
Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father..
File to output the mendelian violation details..
An output file created by the walker. Will overwrite contents if file exists.
Input VCF file. Variants from this VCF file are used by this tool as input. The file must at least contain the standard VCF header lines, but can be empty (i.e., no variants are contained in the file). --variant binds reference ordered data. This argument supports ROD files of the following types: BCF2, VCF, VCF3
GATK version 2.7-4-g46ca8c7 built at 2013/10/10 17:33:37.