Walks 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).
Performs physical phasing of SNP calls, based on sequencing reads.
VCF file of SNP calls, BAM file of sequence reads.
Phased VCF file.
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
These Read Filters are automatically applied to the data by the Engine before processing by ReadBackedPhasing.
This tool applies the following downsampling settings by default.
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||File to which variants should be written|
|--cacheWindowSize||Integer||20000||The window size (in bases) to cache variant sites and their reads for the phasing procedure|
|--maxGenomicDistanceForMNP||int||1||The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record|
|--maxPhaseSites||Integer||10||The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm|
|--min_base_quality_score||int||17||Minimum base quality required to consider a base for phasing|
|--min_mapping_quality_score||int||20||Minimum read mapping quality required to consider a read for phasing|
|--phaseQualityThresh||Double||10.0||The minimum phasing quality score required to output phasing|
|--sampleToPhase||Set[String]||NA||Only include these samples when phasing|
|--debug||boolean||false||If specified, print out very verbose debug information (if -l DEBUG is also specified)|
|-enableMergeToMNP||boolean||false||Merge consecutive phased sites into MNP records|
|--respectPhaseInInput||boolean||false||Will only phase genotypes in cases where the resulting output will necessarily be consistent with any existing phase (for example, from trios)|
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.
If specified, print out very verbose debug information (if -l DEBUG is also specified).
Merge consecutive phased sites into MNP records.
The maximum reference-genome distance between consecutive heterozygous sites to permit merging phased VCF records into a MNP record.
The maximum number of successive heterozygous sites permitted to be used by the phasing algorithm.
Minimum base quality required to consider a base for phasing.
Minimum read mapping quality required to consider a read for phasing.
File to which variants should be written.
The minimum phasing quality score required to output phasing.
Will only phase genotypes in cases where the resulting output will necessarily be consistent with any existing phase (for example, from trios). Important note: do not use this argument if your input data set is not already phased or it will cause the tool to skip over all heterozygous sites.
Only include these samples when phasing.
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 2.8-1-g2a26ec9 built at 2013/12/06 16:54:02.