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ReadBackedPhasing

Annotate physical phasing information

Category Variant Manipulation Tools

Traversal LocusWalker

PartitionBy LOCUS


Overview

This tool identifies haplotypes based on the overlap between reads and uses this information to generate physical phasing information for variants within these haplotypes.

It operates by walking along all variant ROD loci, caching a user-defined window of VariantContext sites, and then finishes phasing them when they go out of range (using upstream and downstream reads). The underlying algorithm is based on building up 2^n local haplotypes, where n is the number of heterozygous SNPs in the local region we expected to find phase-informative reads (and assumes a maximum value of maxPhaseSites, a user parameter). Then, these 2^n haplotypes are used to determine, with sufficient certainty (the assigned PQ score), to which haplotype the alleles of a genotype at a particular locus belong (denoted by the HP tag).

Performs physical phasing of SNP calls, based on sequencing reads.

Input

VCF file of SNP calls, BAM file of sequence reads.

Output

Phased VCF file using HP tags to link alleles at (possibly non-consecutive) genotypes of the same sample.

Example

     GT:GQ:HP    0/1:99:17690409-1,17690409-2
     GT:GQ:HP    0/1:99:17690409-2,17690409-1:1258.14
 

The second site's alternate allele (1) is on the same physical haplotype as the first site's reference allele (0), and vice versa [second site's 0 goes with first site's 1]. This is based on the fact that the HP pairs line up in reverse order between these two genotypes.

In an old notation that RBP used to output in much earlier versions, the genotypes would have been: 0/1 and 1|0, respectively. This was changed because depending on the case it caused ambiguity, incompleteness, and possible inconsistency with trio-based phasing. In contrast, the HP tag is much more explicitl for linking alleles, especially if the genotypes are non-consecutive.

Usage example

    java -jar GenomeAnalysisTK.jar \
      -T ReadBackedPhasing \
      -R reference.fasta \
      -I reads.bam \
      --variant SNPs.vcf \
      -L SNPs.vcf \
      -o phased_SNPs.vcf \
      --phaseQualityThresh 20.0
 

Caveat

The current implementation works for diploid SNPs, and will transparently (but properly) ignore other sites.


Additional Information

Read filters

These Read Filters are automatically applied to the data by the Engine before processing by ReadBackedPhasing.


Command-line Arguments

Engine arguments

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.

ReadBackedPhasing 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
stdout File to which variants should be written
Optional Parameters
--cacheWindowSize
 -cacheWindow
20000 The window size (in bases) to cache variant sites and their reads for the phasing procedure
--maxGenomicDistanceForMNP
 -maxDistMNP
1 The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record
--maxPhaseSites
 -maxSites
10 The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm
--min_base_quality_score
 -mbq
17 Minimum base quality required to consider a base for phasing
--min_mapping_quality_score
 -mmq
20 Minimum read mapping quality required to consider a read for phasing
--phaseQualityThresh
 -phaseThresh
20.0 The minimum phasing quality score required to output phasing
--sampleToPhase
NA Only include these samples when phasing
Optional Flags
--debug
false If specified, print out very verbose debug information (if -l DEBUG is also specified)
--enableMergePhasedSegregatingPolymorphismsToMNP
 -enableMergeToMNP
false Merge consecutive phased sites into MNP records

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.


--cacheWindowSize / -cacheWindow

The window size (in bases) to cache variant sites and their reads for the phasing procedure

Integer  20000  [ [ -∞  ∞ ] ]


--debug / -debug

If specified, print out very verbose debug information (if -l DEBUG is also specified)

boolean  false


--enableMergePhasedSegregatingPolymorphismsToMNP / -enableMergeToMNP

Merge consecutive phased sites into MNP records

boolean  false


--maxGenomicDistanceForMNP / -maxDistMNP

The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record

int  1  [ [ -∞  ∞ ] ]


--maxPhaseSites / -maxSites

The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm

Integer  10  [ [ -∞  ∞ ] ]


--min_base_quality_score / -mbq

Minimum base quality required to consider a base for phasing

int  17  [ [ -∞  ∞ ] ]


--min_mapping_quality_score / -mmq

Minimum read mapping quality required to consider a read for phasing

int  20  [ [ -∞  ∞ ] ]


--out / -o

File to which variants should be written

VariantContextWriter  stdout


--phaseQualityThresh / -phaseThresh

The minimum phasing quality score required to output phasing

Double  20.0  [ [ -∞  ∞ ] ]


--sampleToPhase / -sampleToPhase

Only include these samples when phasing

Set[String]  NA


--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).

This argument supports reference-ordered data (ROD) files in the following formats: BCF2, VCF, VCF3

R RodBinding[VariantContext]  NA


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GATK version 3.6-0-g89b7209 built at 2017/02/09 12:52:48.