# PhaseByTransmission

Computes the most likely genotype combination and phases trios and parent/child pairs

## Overview

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:

• Sites where all individuals are heterozygous
• Sites where there is a Mendelian violation
Missing genotypes are handled as follows:
• In parent/child pairs: If an individual genotype is missing at one site, the other one is phased if it is homozygous. No phasing probability is emitted.
• In trios: If the child is missing, parents are treated as separate individuals and phased if homozygous. No phasing probability is emitted.
• In trios: If one of the parents is missing, it is handled like a parent/child pair. Phasing is done unless both the parent and child are heterozygous and a phasing probability is emitted.
• In trios: If two individuals are missing, the remaining individual is phased if it is homozygous. No phasing probability is emitted.

### Input

• A VCF variant set containing trio(s) and/or parent/child pair(s).
• A PED pedigree file containing the description of the individuals relationships.

## Options

• MendelianViolationsFile: An optional argument for reporting. If a file is specified, all sites that remain in mendelian violation after being assigned the most likely genotype combination will be reported there. Information reported: chromosome, position, filter, allele count in VCF, family, transmission probability, and each individual genotype, depth, allelic depth and likelihoods.
• DeNovoPrior: Mutation prio; default is 1e-8

### Output

An VCF with genotypes recalibrated as most likely under the familial constraint and phased by descent where non ambiguous..

### Examples

 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.

### Downsampling settings

This tool applies the following downsampling settings by default.

• Mode: BY_SAMPLE
• To coverage: 1,000

## Command-line Arguments

### Inherited arguments

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).

### PhaseByTransmission specific arguments

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
Required Inputs
--variant
-V
NA Input VCF file
Optional Outputs
--out
-o
NA 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
NA Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.

### Argument details

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.

### --DeNovoPrior / -prior

Prior for de novo mutations. Default: 1e-8

double  [ [ -∞  ∞ ] ]

### --FatherAlleleFirst / -fatherAlleleFirst

Ouputs the father allele as the first allele in phased child genotype. i.e. father|mother rather than mother|father.

boolean

### --MendelianViolationsFile / -mvf

File to output the mendelian violation details.

PrintStream

### --out / -o

An output file created by the walker. Will overwrite contents if file exists

VariantContextWriter

### --variant / -V

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

R RodBinding[VariantContext]