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Popular tool citations

chevron_left Read quality control Read alignment Alignment evaluation Demultiplexing File indexation File format conversion Statistics for biology Bioinformatics workflows File merging Duplicate read removal File filtering Adapter trimming File sampling File comparison File intersection File parsing-extraction File sorting chevron_right
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Protocols

Picard specifications

Information


Unique identifier OMICS_01066
Name Picard
Alternative names PicardTools, Picard-tools
Software type Toolkit/Suite
Interface Command line interface
Restrictions to use None
Input format SAM, BAM, CRAM, VCF, FASTQ
Output format TXT, VCF, BAM, SAM, FASTQ, BFQ, BAI
Biological technology Illumina
Operating system Unix/Linux
Programming languages Java
License MIT License
Computer skills Advanced
Version 2.0.1
Stability Stable
Requirements
SAMtools/htsjdk
Maintained Yes

Subtools


  • AddCommentsToBam
  • AddOrReplaceReadGroups
  • BaitDesigner
  • BamIndexStats
  • BamToBfq
  • BedToIntervalList
  • BuildBamIndex
  • CalculateReadGroupChecksum
  • CheckFingerprint
  • CheckIlluminaDirectory
  • CheckTerminatorBlock
  • CleanSam
  • ClusterCrosscheckMetrics
  • CollectAlignmentSummaryMetrics
  • CollectBaseDistributionByCycle
  • CollectGcBiasMetrics
  • CollectHiSeqXPfFailMetrics
  • CollectHsMetrics
  • CollectIlluminaBasecallingMetrics
  • CollectIlluminaLaneMetrics
  • CollectInsertSizeMetrics
  • CollectJumpingLibraryMetrics
  • CollectMultipleMetrics
  • CollectOxoGMetrics
  • CollectRawWgsMetrics
  • CollectRnaSeqMetrics
  • CollectRrbsMetrics
  • CollectSequencingArtifactMetrics
  • CollectTargetedPcrMetrics
  • CollectVariantCallingMetrics
  • CollectWgsMetrics
  • CollectWgsMetricsWithNonZeroCoverage
  • CompareMetrics
  • CompareSAMs
  • ConvertSequencingArtifactToOxoG
  • CreateSequenceDictionary
  • CrosscheckFingerprints
  • DownsampleSam
  • EstimateLibraryComplexity
  • ExtractIlluminaBarcodes
  • ExtractSequences
  • FastqToSam
  • FastqToSam
  • FifoBuffer
  • FilterSamReads
  • FilterVcf
  • FindMendelianViolations
  • FixMateInformation
  • GatherBamFiles
  • GatherVcfs
  • GenotypeConcordance
  • IlluminaBasecallsToFastq
  • IlluminaBasecallsToSam
  • IntervalListTools
  • LiftOverIntervalList
  • LiftoverVcf
  • MakeSitesOnlyVcf
  • MarkDuplicates
  • MarkDuplicatesWithMateCigar
  • MarkIlluminaAdapters
  • MeanQualityByCycle
  • MergeBamAlignment
  • MergeSamFiles
  • MergeVcfs
  • NormalizeFasta
  • PositionBasedDownsampleSam
  • QualityScoreDistribution
  • RenameSampleInVcf
  • ReorderSam
  • ReplaceSamHeader
  • RevertOriginalBaseQualitiesAndAddMateCigar
  • RevertSam
  • SamFormatConverter
  • SamToFastq
  • ScatterIntervalsByNs
  • SetNmMdAndUqTags
  • SortSam
  • SortVcf
  • SplitSamByLibrary
  • SplitVcfs
  • UmiAwareMarkDuplicatesWithMateCigar
  • UpdateVcfSequenceDictionary
  • ValidateSamFile
  • VcfFormatConverter
  • ViewSam

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Documentation


Picard citations

 (3516)
library_books

Phenotypic diversification by enhanced genome restructuring after induction of multiple DNA double strand breaks

2018
Nat Commun
PMCID: 5959919
PMID: 29777105
DOI: 10.1038/s41467-018-04256-y

[…] (illumina). for error correction, the miseq data were mapped to the backbone of the assembled contigs using bwa, and then the snps and indels in the backbone contigs were detected and modified by picard (http://broadinstitute.github.io/picard/), gatk, and perl scripts. the contigs were further improved using the gap-closing module in pbjelly (pbsuite 15.8.24), and the sequences were corrected […]

library_books

Auxin decreases chromatin accessibility through the TIR1/AFBs auxin signaling pathway in proliferative cells

2018
Sci Rep
PMCID: 5958073
PMID: 29773913
DOI: 10.1038/s41598-018-25963-y

[…] in the paired-end mode. the reads were mapped to the arabidopsis reference by bowtie 1.2.1 with the following parameters: ‘-m 3 –v 2’. duplicated reads were removed using the default parameters of picard 2.17.11 (http://broadinstitute.github.io/picard/) (table ). macs2 2.1.0 was used to identify the accessible regions and peaks with the following parameters: ‘-nomodel -nolambda -keep-dup […]

library_books

A whole genome sequence study identifies genetic risk factors for neuromyelitis optica

2018
Nat Commun
PMCID: 5955905
PMID: 29769526
DOI: 10.1038/s41467-018-04332-3

[…] and data were collected with informed consent under local irb-approved protocols., sequence reads were processed and aligned to the reference genome (hg19) with the bwa algorithm and processed with picard (http://picard.sourceforge.net). polymorphic snp and indel sites and genotypes were called with the haplotypecaller from gatk v3.1–. the haplotypecaller algorithm is an assembly-based method […]

library_books

Genomic alterations of ground glass nodular lung adenocarcinoma

2018
Sci Rep
PMCID: 5955945
PMID: 29769567
DOI: 10.1038/s41598-018-25800-2

[…] rapid pe cluster kit and truseq rapid sbs kit (illumina)., sequence reads were mapped to the human genome (hg19) using burrows-wheeler alignment tool. duplicate read removal was performed using picard and samtools, and local alignment was optimized by the genome analysis toolkit. variant calling was only performed in targeted regions of cancerscan. somatic variant calling of each tumor […]

library_books

Comparative Genomics Reveals the Core Gene Toolbox for the Fungus Insect Symbiosis

2018
MBio
PMCID: 5954228
PMID: 29764946
DOI: 10.1128/mBio.00636-18

[…] 1,000 replications with the iq-tree tool (55 of the 582 alignments were discarded due to having a length shorter than 50 aa)., the whole-genome-wide snps were identified using bwa (), samtools (), picard tools (http://broadinstitute.github.io/picard), and the gatk toolkit (), according to the previously described pipeline method (). a total of 460 to 484 single-copy orthologs among the nine […]

library_books

Copy number variants implicate cardiac function and development pathways in earthquake induced stress cardiomyopathy

2018
Sci Rep
PMCID: 5954162
PMID: 29765130
DOI: 10.1038/s41598-018-25827-5

[…] included removal of reads from duplicate fragments, realignment around known indels, and recalibration of all base quality scores. read depth and coverage for all exome datasets were derived using picard collecthsmetrics function. on average, 22.7 million reads (range 16.9–30.7 m) at mean quality scores (phred) of q37 were mapped to the exome target intervals; 70% (range 61–77%) of targeted […]


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Picard institution(s)
Broad Institute, MA, USA

Picard review

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Arup Ghosh

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Sort, filter, merge, randomize SAM/BAM/CRAM and VCF files.