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

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

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

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

ClearDuplicateFlag clear the duplicate flag in every read.

CombineVcfOutputs combines multiple VCF files.

FilterReadsBySampleName filters out reads that do not belong to exactly one sample.

HaplotypeCallAln filters out the reads that the haplotypecaller cannot process.

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

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

LoadAndCombineDuplicateMetrics loads partial duplication metrics from file and combines them.

MarkDuplicates returns a filter for marking duplicate alignments.

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

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

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

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

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

PrintDuplicatesMetricsToIntermediateFile writes the duplicate metrics to a gob file.

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

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

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).

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).

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

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

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

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

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

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

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

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

AC represents allele count in genotypes for each ALT allele in VCF files.

AD represents allelic depths in VCF files.

AF represents allele frequency for each ALT allele in VCF files.

AN represents total number of alleles in called genotypes in VCF files.

BaseQRankSum represents rank sum test of alt vs ref base qualities in VCF files.

DP represenst depth in VCF files.

ExcessHet represenst Excess Heterozygosity in VCF files.

FS represents phred-scaled p-value using Fisher's exact test to detect strand bias in VCF files.

GQ represents genotype quality in VCF files.

LowQual represents low quality variants in VCF files.

MIN_DP represents minimum depths in GVCF blocks in VCF files.

MLEAC represenst the maximum likelihood expectation for the allele count in VCF files.

MLEAF represents the maximum likelihood expectation for the allele frequency in VCF files.

MQ represents root mean square of mapping quality in VCF files.

MQRankSum represents rank sum test of alt vs ref read mapping qualities in VCF files.

PGT is the HaplotypeCaller phasing genotype.

PID is the HaplotypeCaller phasing ID.

PL represents likelihoods for genotypes in VCF files.

PS is the HaplotypeCaller phasing set ID.

QD represents variant confidence/quality by depth in VCF files.

Raw_MQandDP represents raw squared mapping quality and depth in VCF files.

ReadPosRankSum represents rank sum test of alt vs ref read position bias in VCF files.

SB represents strand bias in VCF files.

SOR represents symmetric odds ratio of 2x2 contingency table to detect strand bias in VCF files.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

Symbols for optional fields used for determining exact matches.

BaseRecalibrator implements the first step of base recalibration.

BaseRecalibratorTables is the result of the base recalibration.

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