filters

package
v5.1.3 Latest Latest
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 Go to latest Published: Apr 27, 2022 License: AGPL-3.0, AGPL-3.0-or-later Imports: 28 Imported by: 0

Documentation

Overview

Package filters defines filters for .sam/.bam sequencing pipelines.

Index

Constants

View Source 
const FixedHighQDMessage = ""

Variables

View Source 
var (
	// PID is the HaplotypeCaller phasing ID.
	PID = utils.Intern("PID")
	// PGT is the HaplotypeCaller phasing genotype.
	PGT = utils.Intern("PGT")
	// PS is the HaplotypeCaller phasing set ID.
	PS = utils.Intern("PS")
)
View Source 
var (
	// DP represenst depth in VCF files.
	DP = utils.Intern("DP")

	// ExcessHet represenst Excess Heterozygosity in VCF files.
	ExcessHet = utils.Intern("ExcessHet")
	// MLEAC represenst the maximum likelihood expectation for the allele count in VCF files.
	MLEAC = utils.Intern("MLEAC")
	// MLEAF represents the maximum likelihood expectation for the allele frequency in VCF files.
	MLEAF = utils.Intern("MLEAF")
	// LowQual represents low quality variants in VCF files.
	LowQual = utils.Intern("LowQual")
	// Raw_MQandDP represents raw squared mapping quality and depth in VCF files.
	RAW_MQandDP = utils.Intern("RAW_MQandDP")
	// MQ represents root mean square of mapping quality in VCF files
	MQ = utils.Intern("MQ")
	// BaseQRankSum represents rank sum test of alt vs ref base qualities in VCF files.
	BaseQRankSum = utils.Intern("BaseQRankSum")
	// MQRankSum represents rank sum test of alt vs ref read mapping qualities in VCF files.
	MQRankSum = utils.Intern("MQRankSum")
	// ReadPosRankSum represents rank sum test of alt vs ref read position bias in VCF files.
	ReadPosRankSum = utils.Intern("ReadPosRankSum")

	// AC represents allele count in genotypes for each ALT allele in VCF files.
	AC = utils.Intern("AC")
	// AF represents allele frequency for each ALT allele in VCF files.
	AF = utils.Intern("AF")
	// AN represents total number of alleles in called genotypes in VCF files.
	AN = utils.Intern("AN")

	AD = utils.Intern("AD")
	// GQ represents genotype quality in VCF files.
	GQ = utils.Intern("GQ")
	// MIN_DP represents minimum depths in GVCF blocks in VCF files.
	MIN_DP = utils.Intern("MIN_DP")
	// PL represents likelihoods for genotypes in VCF files.
	PL = utils.Intern("PL")
	// SB represents strand bias in VCF files.
	SB = utils.Intern("SB")

	// FS represents phred-scaled p-value using Fisher's exact test to detect strand bias in VCF files.
	FS = utils.Intern("FS")
	// QD represents variant confidence/quality by depth in VCF files.
	QD = utils.Intern("QD")
	// SOR represents symmetric odds ratio of 2x2 contingency table to detect strand bias in VCF files.
	SOR = utils.Intern("SOR")
)
View Source 
var (
	X0 = utils.Intern("X0")
	X1 = utils.Intern("X1")
	XM = utils.Intern("XM")
	XO = utils.Intern("XO")
	XG = utils.Intern("XG")
)

Symbols for optional fields used for determining exact matches. See http://samtools.github.io/hts-specs/SAMv1.pdf - Section 1.5.

Functions

func AddOrReplaceReadGroup 

func AddOrReplaceReadGroup(readGroup utils.StringMap) sam.Filter

AddOrReplaceReadGroup returns a filter for adding or replacing the read group both in the Header and in each Alignment.

func AddPGLine 

func AddPGLine(newPG utils.StringMap) sam.Filter

AddPGLine returns a filter for adding a @PG tag to a Header, and ensuring that it is the first one in the chain.

func AddREFID 

func AddREFID(header *sam.Header) sam.AlignmentFilter

AddREFID is a filter for adding the refid (index in the reference sequence dictionary) to alignments as temporary values.

func CleanSam 

func CleanSam(header *sam.Header) sam.AlignmentFilter

CleanSam is a filter for soft-clipping an alignment at the end of a reference sequence, and setting MAPQ to 0 if unmapped.

func ClearDuplicateFlag 

func ClearDuplicateFlag(_ *sam.Header) sam.AlignmentFilter

ClearDuplicateFlag clear the duplicate flag in every read

func CombineVcfOutputs 

func CombineVcfOutputs(vcfPath, vcfOutput string)

CombineVcfOutputs combines multiple VCF files. This is used in the sfm command.

func FilterReadsBySampleName 

func FilterReadsBySampleName(sampleName *string) sam.Filter

FilterReadsBySampleName filters out reads that do not belong to exactly one sample. If *sampleName != "", ensure only reads are passed through that match this sample name. If *sampleName == "", check that the header has only one (or no) sample name, and don't filter reads. In the latter case, after use of this filter in a pipeline, *sampleName will contain the unique sample name detected from the header, if any.

func HaplotypeCallAln 

func HaplotypeCallAln(hdr *sam.Header) sam.AlignmentFilter

HaplotypeCallAln filters out the reads that the haplotypecaller cannot process.

func KeepOptionalFields 

func KeepOptionalFields(tags []string) sam.Filter

KeepOptionalFields returns a filter for removing all but a list of given optional fields in an alignment.

func LoadAndCombineDuplicateMetrics 

func LoadAndCombineDuplicateMetrics(metricsPath string) map[string]*DuplicatesCtr

LoadAndCombineDuplicateMetrics loads partial duplication metrics from file and combines them

func MarkDuplicates 

func MarkDuplicates(alsoOpticals bool) (sam.Filter, *sync.Map, *sync.Map)

MarkDuplicates returns a filter for marking duplicate alignments. Depends on the AddREFID filter being called before to fill in the refid.

Duplicate marking is based on an adapted Phred score. In case of ties, the QNAME is used as a tie-breaker.

If alsoOpticals is true, ensure that LIBID is added for all reads.

func MarkOpticalDuplicates 

func MarkOpticalDuplicates(reads *sam.Sam, pairs *sync.Map, opticalPixelDistance int) map[string]*DuplicatesCtr

MarkOpticalDuplicates implements a function for calculating duplication metrics for a set of reads.

func PrintDuplicatesMetrics 

func PrintDuplicatesMetrics(metrics, commandLine string, ctrs map[string]*DuplicatesCtr)

PrintDuplicatesMetrics writes the duplication metrics for a set of reads to a file.

func PrintDuplicatesMetricsToIntermediateFile 

func PrintDuplicatesMetricsToIntermediateFile(name string, ctrs map[string]*DuplicatesCtr)

PrintDuplicatesMetricsToIntermediateFile writes the duplicate metrics to a gob file.

func RemoveDuplicateReads 

func RemoveDuplicateReads(_ *sam.Header) sam.AlignmentFilter

RemoveDuplicateReads is a filter for removing duplicate sam-alignment instances, based on FLAG.

func RemoveMappingQualityLessThan 

func RemoveMappingQualityLessThan(mq int) sam.Filter

RemoveMappingQualityLessThan is a filter for removing reads that do not match or exceed the given mapping quality.

func RemoveNonExactMappingReads 

func RemoveNonExactMappingReads(_ *sam.Header) sam.AlignmentFilter

RemoveNonExactMappingReads is a filter that removes all reads that are not exact matches with the reference (soft-clipping ok), based on CIGAR string (only M and S allowed).

func RemoveNonExactMappingReadsStrict 

func RemoveNonExactMappingReadsStrict(header *sam.Header) sam.AlignmentFilter

RemoveNonExactMappingReadsStrict is a filter that removes all reads that are not exact matches with the reference, based on the optional fields X0=1 (unique mapping), X1=0 (no suboptimal hit), XM=0 (no mismatch), XO=0 (no gap opening), XG=0 (no gap extension).

func RemoveNonOverlappingReads 

func RemoveNonOverlappingReads(bed bed.Bed) sam.Filter

RemoveNonOverlappingReads returns a filter for removing all reads that do not overlap with a set of regions specified by a bed file.

func RemoveOptionalFields 

func RemoveOptionalFields(tags []string) sam.Filter

RemoveOptionalFields returns a filter for removing optional fields in an alignment.

func RemoveOptionalReads 

func RemoveOptionalReads(header *sam.Header) sam.AlignmentFilter

RemoveOptionalReads is a filter for removing alignments that represent optional information in elPrep.

func RemoveUnmappedReads 

func RemoveUnmappedReads(_ *sam.Header) sam.AlignmentFilter

RemoveUnmappedReads is a filter for removing unmapped sam-alignment instances, based on FLAG.

func RemoveUnmappedReadsStrict 

func RemoveUnmappedReadsStrict(_ *sam.Header) sam.AlignmentFilter

RemoveUnmappedReadsStrict is a filter for removing unmapped sam-alignment instances, based on FLAG, or POS=0, or RNAME=*.

func RenameChromosomes 

func RenameChromosomes(header *sam.Header) sam.AlignmentFilter

RenameChromosomes is a filter for prepending "chr" to the reference sequence names in a Header, and in RNAME and RNEXT in each Alignment.

func ReplaceReferenceSequenceDictionary 

func ReplaceReferenceSequenceDictionary(dict []utils.StringMap) sam.Filter

ReplaceReferenceSequenceDictionary returns a filter for replacing the reference sequence dictionary in a Header.

func ReplaceReferenceSequenceDictionaryFromSamFile 

func ReplaceReferenceSequenceDictionaryFromSamFile(samFile string) sam.Filter

ReplaceReferenceSequenceDictionaryFromSamFile returns a filter for replacing the reference sequence dictionary in a Header with one parsed from the given SAM/DICT file.

Types

type BaseRecalibrator 

type BaseRecalibrator struct {
	// contains filtered or unexported fields
}

BaseRecalibrator implements the first step of base recalibration.

func NewBaseRecalibrator 

func NewBaseRecalibrator(knownSites []string, referenceFasta *fasta.MappedFasta) (recal *BaseRecalibrator)

NewBaseRecalibrator returns a struct for the first step of base recalibration.

func (*BaseRecalibrator) Recalibrate 

func (recal *BaseRecalibrator) Recalibrate(reads *sam.Sam, maxCycle int) *BaseRecalibratorTables

Recalibrate implements the first step of base recalibration.

type BaseRecalibratorTables 

type BaseRecalibratorTables struct {
	QualityScores, Cycles, Contexts bqsrTable
}

BaseRecalibratorTables is the result of the base recalibration. All subsequent steps, including ApplyBQSR, are based on these tables.

func LoadAndCombineBQSRTables 

func LoadAndCombineBQSRTables(bqsrPath string) *BaseRecalibratorTables

LoadAndCombineBQSRTables loads and merges multiple recalibration tables from file into a single, new recalibration table.

func NewBaseRecalibratorTables 

func NewBaseRecalibratorTables() BaseRecalibratorTables

NewBaseRecalibratorTables returns a struct for storing the result of the base recalibration.

func (*BaseRecalibratorTables) ApplyBQSR 

func (recal *BaseRecalibratorTables) ApplyBQSR(quantizeLevels int, sqqList []uint8, maxCycle int) sam.Filter

ApplyBQSR applies the base recalibration result to the QUAL strings of the given reads.

func (*BaseRecalibratorTables) FinalizeBQSRTables 

func (recal *BaseRecalibratorTables) FinalizeBQSRTables()

FinalizeBQSRTables finalizes the first step of base recalibration.

func (*BaseRecalibratorTables) PrintBQSRTables 

func (recal *BaseRecalibratorTables) PrintBQSRTables(name string)

PrintBQSRTables creates a recalibration report file.

func (*BaseRecalibratorTables) PrintBQSRTablesToIntermediateFile 

func (recal *BaseRecalibratorTables) PrintBQSRTablesToIntermediateFile(name string)

PrintBQSRTablesToIntermediateFile prints the recalibration tables to a gob file.

type DuplicatesCtr 

type DuplicatesCtr struct {
	UnpairedReadsExamined         int
	ReadPairsExamined             int
	SecondaryOrSupplementaryReads int
	UnmappedReads                 int
	UnpairedReadDuplicates        int
	ReadPairDuplicates            int
	ReadPairOpticalDuplicates     int
	// contains filtered or unexported fields
}

DuplicatesCtr implements a struct that stores metrics about reads such as the number of (optical) duplicates, unmapped reads, etc.

type HaplotypeCaller 

type HaplotypeCaller struct {
	// contains filtered or unexported fields
}

parameters that influence how assembly regions are determined

func NewHaplotypeCaller 

func NewHaplotypeCaller(
	reference *fasta.MappedFasta,
	referenceConfidence string,
	assemblyRegionPadding int32,
	activityProfile, assemblyRegions io.Writer,
	randomSeedFile string,
	commandLine string) *HaplotypeCaller

NewHaplotypeCaller creates an object that contains the relevent parameters for the haplotypecaller.

func (*HaplotypeCaller) CallVariants 

func (hc *HaplotypeCaller) CallVariants(input *sam.Sam, sampleName, vcfOutput string, bedRegions bed.Bed)

CallVariants is the main entry point into the haplotypecaller.

func (*HaplotypeCaller) Close 

func (hc *HaplotypeCaller) Close()

Source Files

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