Compute the most likely genotype combination and phasing for trios and parent/child pairs
This tool performs two functions:
The tool ultimately reports the genotype combination (and hence phasing) probability.
An VCF with genotypes recalibrated as most likely under the familial constraint and phased by descent (where non ambiguous).
java -jar GenomeAnalysisTK.jar \ -T PhaseByTransmission \ -R reference.fasta \ -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.
All tools inherit arguments from the GATK Engine' "CommandLineGATK" argument collection, which can be used to modify various aspects of the tool's function. For example, the -L argument directs the GATK engine to restrict processing to specific genomic intervals; or the -rf argument allows you to apply certain read filters to exclude some of the data from the analysis.
This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.
|Argument name(s)||Default value||Summary|
|NA||Input VCF file|
|stdout||An output file created by the walker. Will overwrite contents if file exists|
|1.0E-8||Prior for de novo mutations. Default: 1e-8|
|NA||File to output the mendelian violation details.|
|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
double 1.0E-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).
This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3
R RodBinding[VariantContext] NA
GATK version 3.8-0-ge9d806836 built at 2017/07/29 01:40:22.