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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Prints a SAM or BAM file to the screen.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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"

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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