Annotate physical phasing information
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.
VCF file of SNP calls, BAM file of sequence reads.
Phased VCF file using HP tags to link alleles at (possibly non-consecutive) genotypes of the same sample.
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 explicit for linking alleles, especially if the genotypes are non-consecutive.
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
The current implementation works for diploid SNPs, and will transparently (but properly) ignore other sites.
These Read Filters are automatically applied to the data by the Engine before processing by ReadBackedPhasing.
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 | |
|---|---|---|---|
| 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 | |
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.
The window size (in bases) to cache variant sites and their reads for the phasing procedure
Integer 20000 [ [ -∞ ∞ ] ]
If specified, print out very verbose debug information (if -l DEBUG is also specified)
boolean false
Merge consecutive phased sites into MNP records
boolean false
The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record
int 1 [ [ -∞ ∞ ] ]
The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm
Integer 10 [ [ -∞ ∞ ] ]
Minimum base quality required to consider a base for phasing
int 17 [ [ -∞ ∞ ] ]
Minimum read mapping quality required to consider a read for phasing
int 20 [ [ -∞ ∞ ] ]
File to which variants should be written
VariantContextWriter stdout
The minimum phasing quality score required to output phasing
Double 20.0 [ [ -∞ ∞ ] ]
Only include these samples when phasing
Set[String] NA
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