The following tools are available in fgbio version 0.8.1.
Tools for manipulating basecalling data.
|ExtractBasecallingParamsForPicard||Extracts sample and library information from an sample sheet for a given lane|
|ExtractIlluminaRunInfo||Extracts information about an Illumina sequencing run from the RunInfo|
Tools for manipulating FASTA files.
|HardMaskFasta||Converts soft-masked sequence to hard-masked in a FASTA file|
Tools for manipulating FASTQ files.
|DemuxFastqs||Performs sample demultiplexing on FASTQs|
|FastqToBam||Generates an unmapped BAM (or SAM or CRAM) file from fastq files|
|SortFastq||Sorts a FASTQ file|
|TrimFastq||Trims reads in one or more line-matched fastq files to a specific read length|
Various personal programs (not supported).
|FindSwitchbackReads||Finds reads where a template switch occurred during library construction|
|GenerateRegionsFromFasta||Generates a list of ‘freebayes’/’bamtools’ region specifiers|
|SplitTag||Splits an optional tag in a SAM or BAM into multiple optional tags|
|StripFastqReadNumbers||Removes trailing /# from read names in fastq|
Tools for RNA-Seq data
|CollectErccMetrics||Collects metrics for ERCC spike-ins for RNA-Seq experiments|
|EstimateRnaSeqInsertSize||Computes the insert size for RNA-Seq experiments|
Tools for manipulating SAM, BAM, or related data.
|AnnotateBamWithUmis||Annotates existing BAM files with UMIs (Unique Molecular Indices, aka Molecular IDs, Molecular barcodes) from a separate FASTQ file|
|AutoGenerateReadGroupsByName||Adds read groups to a BAM file for a single sample by parsing the read names|
|ClipBam||Clips reads from the same template|
|ErrorRateByReadPosition||Calculates the error rate by read position on coordinate sorted mapped BAMs|
|EstimatePoolingFractions||Examines sequence data generated from a pooled sample and estimates the fraction of sequence data coming from each constituent sample|
|ExtractUmisFromBam||Extracts unique molecular indexes from reads in a BAM file into tags|
|FilterBam||Filters reads out of a BAM file|
|FindTechnicalReads||Find reads that are from technical or synthetic sequences in a BAM file|
|RandomizeBam||Randomizes the order of reads in a SAM or BAM file|
|RemoveSamTags||Removes SAM tags from a SAM or BAM file|
|SetMateInformation||Adds and/or fixes mate information on paired-end reads|
|SortBam||Sorts a SAM or BAM file|
|SplitBam||Splits a BAM into multiple BAMs, one per-read group (or library)|
|TrimPrimers||Trims primers from reads post-alignment|
|UpdateReadGroups||Updates one or more read groups and their identifiers|
Tools for manipulating UMIs & reads tagged with UMIs
|CallDuplexConsensusReads||Calls duplex consensus sequences from reads generated from the same double-stranded source molecule|
|CallMolecularConsensusReads||Calls consensus sequences from reads with the same unique molecular tag|
|CollectDuplexSeqMetrics||Collects a suite of metrics to QC duplex sequencing data|
|CorrectUmis||Corrects UMIs stored in BAM files when a set of fixed UMIs is in use|
|FilterConsensusReads||Filters consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads|
|GroupReadsByUmi||Groups reads together that appear to have come from the same original molecule|
|ReviewConsensusVariants||Extracts data to make reviewing of variant calls from consensus reads easier|
Various utility programs.
|PickIlluminaIndices||Picks a set of molecular indices that should work well together|
|PickLongIndices||Picks a set of molecular indices that have at least a given number of mismatches between them|
Tools for manipulating VCF, BCF, or related data.
|AssessPhasing||Assess the accuracy of phasing for a set of variants|
|FilterSomaticVcf||Applies one or more filters to a VCF of somatic variants|
|HapCutToVcf||Converts the output of ‘HAPCUT’ (‘HapCut1’/’HapCut2’) to a VCF|
|MakeMixtureVcf||Creates a VCF with one sample whose genotypes are a mixture of other samples’|
|MakeTwoSampleMixtureVcf||Creates a simulated tumor or tumor/normal VCF by in-silico mixing genotypes from two samples|