Identifier: TL_e24fa5.c8


A set of command line tools for manipulating high-throughput sequencing (HTS) data in formats such as SAM/BAM/CRAM and VCF. Available as a standalone program or within the GATK4 program.


  • picard GatherVcfs

    Gathers multiple VCF files from a scatter operation into a single VCF file. Input files must be supplied in genomic order and must not have events at

  • picard SamFormatConverter

    Convert a BAM file to a SAM file, or SAM to BAM. Input and output formats are determined by file extension.

  • picard GenotypeConcordance

    Evaluate genotype concordance between callsets. This tool evaluates the concordance between genotype calls for samples in different callsets where one

  • picard RenameSampleInVcf

    Renames a sample within a VCF or BCF. This tool enables the user to rename a sample in either a VCF or BCF file. It is intended to change the name of

  • picard VcfToIntervalList

    Converts a VCF or BCF file to a Picard Interval List.

  • picard AddCommentsToBam

    Adds comments to the header of a BAM file. This tool makes a copy of the input bam file, with a modified header that includes the comments specified a

  • picard BamToBfq

    Create BFQ files from a BAM file for use by the maq aligner. BFQ is a binary version of the FASTQ file format. This tool creates bfq files from a BAM

  • picard ReorderSam

    Not to be confused with SortSam which sorts a SAM or BAM file with a valid sequence dictionary, ReorderSam reorders reads in a SAM/BAM file to match t

  • picard ReplaceSamHeader

    Replaces the SAMFileHeader in a SAM or BAM file. This tool makes it possible to replace the header of a SAM or BAM file with the header of anotherfile

  • picard RevertSam

    Reverts SAM or BAM files to a previous state. This tool removes or restores certain properties of the SAM records, including alignment information, wh

  • picard SetNmMdAndUqTags

    Fixes the NM, MD, and UQ tags in a SAM file. This tool takes in a SAM or BAM file (sorted by coordinate) and calculates the NM, MD, and UQ tags by com

  • picard SortSam

    Sorts a SAM or BAM file. This tool sorts the input SAM or BAM file by coordinate, queryname (QNAME), or some other property of the SAM record. The Sor

  • picard SortVcf

    Sorts one or more VCF files. This tool sorts the records in VCF files according to the order of the contigs in the header/sequence dictionary and then

  • picard SplitSamByLibrary

    Takes a SAM or BAM file and separates all the reads into one SAM or BAM file per library name. Reads that do not have a read group specified or whose

  • picard SplitVcfs

    Splits SNPs and INDELs into separate files. This tool reads in a VCF or BCF file and writes out the SNPs and INDELs it contains to separate files. The

  • picard FilterVcf

    Applies one or more hard filters to a VCF file to filter out genotypes and variants.

  • picard ViewSam

    Prints a SAM or BAM file to the screen.

  • picard FifoBuffer

    Provides a large, configurable, FIFO buffer that can be used to buffer input and output streams between programs with a buffer size that is larger tha

  • picard UpdateVcfSequenceDictionary

    Takes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.

  • picard SamToFastq

    Converts a SAM or BAM file to FASTQ. This tool extracts read sequences and base quality scores from the input SAM/BAM file and outputs them in FASTQ f

  • picard LiftOverIntervalList

    Lifts over an interval list from one reference build to another. This tool adjusts the coordinates in an interval list derived from one reference to m

  • picard VcfFormatConverter

    Converts VCF to BCF or BCF to VCF. This tool converts files between the plain-text VCF format and its binary compressed equivalent, BCF. Input and out

  • picard RevertOriginalBaseQualitiesAndAddMateCigar

    Reverts the original base qualities and adds the mate cigar tag to read-group BAMs.

  • picard CollectInsertSizeMetrics

    This tool provides useful metrics for validating library construction including the insert size distribution and read orientation of paired-end librar

  • picard MeanQualityByCycle

    Collect mean quality by cycle. This tool generates a data table and chart of mean quality by cycle from a BAM file. It is intended to be used on a sin

  • picard CollectJumpingLibraryMetrics

    Collect jumping library metrics. This tool collects high-level metrics about the presence of outward-facing (jumping) and inward-facing (non-jumping)

  • picard CheckFingerprint

    Computes a fingerprint from the supplied input file (SAM/BAM or VCF) file and compares it to the expected fingerprint genotypes provided. The key outp

  • picard CollectVariantCallingMetrics

    Collects per-sample and aggregate (spanning all samples) metrics from the provided VCF file.

  • picard ScatterIntervalsByNs

    Writes an interval list based on splitting a reference by Ns. This tool identifies positions in a reference where the bases are 'no-calls' and writes

  • picard AddOrReplaceReadGroups

    Replace read groups in a BAM file. This tool enables the user to replace all read groups in the INPUT file with a single new read group and assign all

  • picard BaitDesigner

    Designs oligonucleotide baits for hybrid selection reactions. This tool is used to design custom bait sets for hybrid selection experiments. The follo

  • picard BamIndexStats

    Generate index statistics from a BAM fileThis tool calculates statistics from a BAM index (.bai) file, emulating the behavior of the "samtools idxstat

  • picard BedToIntervalList

    Converts a BED file to a Picard Interval List. This tool provides easy conversion from BED to the Picard interval_list format which is required by man

  • picard BuildBamIndex

    Generates a BAM index ".bai" file. This tool creates an index file for the input BAM that allows fast look-up of data in a BAM file, lke an index on a

  • picard CalculateReadGroupChecksum

    Creates a hash code based on the read groups (RG). This tool creates a hash code based on identifying information in the read groups (RG) of a ".BAM"

  • picard CheckIlluminaDirectroy

    Asserts the validity for specified Illumina basecalling data. This tool will check that the basecall directory and the internal files are available, e

  • picard CheckTerminatorBlock

    Asserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise

  • picard CleanSam

    Cleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads

  • picard ClusterCrosscheckMetrics

    Clusters the results from a CrosscheckFingerprints into groups that are connected according to a large enough LOD score.

  • picard CollectAlignmentSummaryMetrics

    Produces a summary of alignment metrics from a SAM or BAM file. This tool takes a SAM/BAM file input and produces metrics detailing the quality of the

  • picard CollectIlluminaBasecallingMetrics

    Collects Illumina Basecalling metrics for a sequencing run. This tool will produce per-barcode and per-lane basecall metrics for each sequencing run.

  • picard CollectIlluminaLaneMetrics

    Collects Illumina lane metrics for the given BaseCalling analysis directory. This tool produces quality control metrics on cluster density for each la

  • picard CollectBaseDistributionByCycle

    Chart the nucleotide distribution per cycle in a SAM or BAM fileThis tool produces a chart of the nucleotide distribution per cycle in a SAM or BAM fi

  • picard CollectGcBiasMetrics

    Collect metrics regarding GC bias. This tool collects information about the relative proportions of guanine (G) and cytosine (C) nucleotides in a samp

  • picard CollectHiSeqXPfFailMetrics

    Classify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories. This tool categorizes the reads that did not pass filter

  • picard CollectWgsMetrics

    Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. This tool collects metrics about the fractions of reads t

  • picard CollectHsMetrics

    Collects hybrid-selection (HS) metrics for a SAM or BAM file. This tool takes a SAM/BAM file input and collects metrics that are specific for sequence

  • picard CollectMultipleMetrics

    Collect multiple classes of metrics. This 'meta-metrics' tool runs one or more of the metrics collection modules at the same time to cut down on the t

  • picard CollectOxoGMetrics

    Collect metrics to assess oxidative artifacts. This tool collects metrics quantifying the error rate resulting from oxidative artifacts. For a brief p

  • picard CollectQualityYieldMetrics

    Collect metrics about reads that pass quality thresholds and Illumina-specific filters. This tool evaluates the overall quality of reads within a bam

  • picard CollectRawWgsMetrics

    Collect whole genome sequencing-related metrics. This tool computes metrics that are useful for evaluating coverage and performance of whole genome se

  • picard CollectRnaSeqMetrics

    Produces RNA alignment metrics for a SAM or BAM file. This tool takes a SAM/BAM file containing the aligned reads from an RNAseq experiment and produc

  • picard CollectRrbsMetrics

    Collects metrics from reduced representation bisulfite sequencing (Rrbs) data. This tool uses reduced representation bisulfite sequencing (Rrbs) data

  • picard CollectSequencingArtifactMetrics

    Collect metrics to quantify single-base sequencing artifacts. This tool examines two sources of sequencing errors associated with hybrid selection pro

  • picard CollectTargetedPcrMetrics

    Calculate PCR-related metrics from targeted sequencing data. This tool calculates a set of PCR-related metrics from an aligned SAM or BAM file contain

  • picard CollectWgsMetricsWithNonZeroCoverage

    Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. This tool collects metrics about the percentages of reads

  • picard CompareMetrics

    Compare two metrics files.This tool compares the metrics and histograms generated from metric tools to determine if the generated results are identica

  • picard CompareSAMs

    Compare two input ".sam" or ".bam" files. This tool initially compares the headers of SAM or BAM files. If the file headers are comparable, the tool w

  • picard ConvertSequencingArtifactToOxoG

    Extract OxoG metrics from generalized artifacts metrics. This tool extracts 8-oxoguanine (OxoG) artifact metrics from the output of CollectSequencingA

  • picard CreateSequenceDictionary

    Creates a sequence dictionary for a reference sequence. This tool creates a sequence dictionary file (with ".dict" extension) from a reference sequenc

  • picard CrosscheckFingerprints

    Checks if all fingerprints within a set of files appear to come from the same individual. The fingerprints are calculated initially at the readgroup l

  • picard GatherBamFiles

    Concatenate one or more BAM files as efficiently as possibleThis tool performs a rapid "gather" operation on BAM files after scatter operations where

  • picard DownsampleSam

    Downsample a SAM or BAM file. This tool applies a random downsampling algorithm to a SAM or BAM file to retain only a random subset of the reads. Read

  • picard EstimateLibraryComplexity

    Estimates the numbers of unique molecules in a sequencing library. This tool outputs quality metrics for a sequencing library preparation. Library com

  • picard ExtractIlluminaBarcodes

    Tool determines the barcode for each read in an Illumina lane. This tool determines the numbers of reads containing barcode-matching sequences and pro

  • picard ExtractSequences

    Subsets intervals from a reference sequence to a new FASTA file. This tool takes a list of intervals, reads the corresponding subsquences from a refer

  • picard FastqToSam

    Converts a FASTQ file to an unaligned BAM or SAM file. This tool extracts read sequences and base qualities from the input FASTQ file and writes them

  • picard FilterSamReads

    Subset read data from a SAM or BAM fileThis tool takes a SAM or BAM file and subsets it to a new file that either excludes or only includes either ali

  • picard FindMedelianViolations

    Finds mendelian violations of all types within a VCF. Takes in VCF or BCF and a pedigree file and looks for high confidence calls where the genotype o

  • picard FixMateInformation

    Verify mate-pair information between mates and fix if needed. This tool ensures that all mate-pair information is in sync between each read and its ma

  • picard IlluminaBasecallsToFastq

    Generate FASTQ file(s) from Illumina basecall read data. This tool generates FASTQ files from data in an Illumina BaseCalls output directory. Separate

  • picard IluminaBasecallsToSam

    Transforms raw Illumina sequencing data into an unmapped SAM or BAM file. The IlluminaBaseCallsToSam program collects, demultiplexes, and sorts reads

  • picard IntervalListTools

    Manipulates interval lists. This tool offers multiple interval list file manipulation capabilities include sorting, merging, subtracting, padding, cus

  • picard LiftoverVcf

    Lifts over a VCF file from one reference build to another. This tool adjusts the coordinates of variants within a VCF file to match a new reference. T

  • picard MakeSitesOnlyVcf

    Reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information, including annotations based on genotyp

  • picard MarkDuplicates

    Identifies duplicate reads. This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a s

  • picard MarkDuplicatesWithMateCigar

    Identifies duplicate reads, accounting for mate CIGAR. This tool locates and tags duplicate reads (both PCR and optical) in a BAM or SAM file, where d

  • picard MarkIlluminaAdapters

    Reads a SAM or BAM file and rewrites it with new adapter-trimming tags. This tool clears any existing adapter-trimming tags (XT:i:) in the optional ta

  • picard MergeBamAlignment

    Merge alignment data from a SAM or BAM with data in an unmapped BAM file. This tool produces a new SAM or BAM file that includes all aligned and unali

  • picard MergeSamFiles

    Merges multiple SAM and/or BAM files into a single file. This tool is used for combining SAM and/or BAM files from different runs or read groups, simi

  • picard MergeVcfs

    Merges multiple VCF or BCF files into one VCF file. Input files must be sorted by their contigs and, within contigs, by start position. The input file

  • picard NormalizeFasta

    Normalizes lines of sequence in a FASTA file to be of the same length.This tool takes any FASTA-formatted file and reformats the sequence to ensure th

  • picard PositionBasedDownsampleSam

    Class to downsample a BAM file while respecting that we should either get rid of both ends of a pair or neither end of the pair. In addition, this pro

  • picard QualityScoreDistribution

    Chart the distribution of quality scores. This tool is used for determining the overall 'quality' for a library in a given run. To that effect, it out

  • picard UmiAwareMarkDuplicatesWithMateCigar

    Identifies duplicate reads using information from read positions and UMIs. This tool locates and tags duplicate reads in a BAM or SAM file, where dupl

  • picard ValidateSamFile

    Validates a SAM or BAM file. This tool reports on the validity of a SAM or BAM file relative to the SAM format specification. This is useful for troub