Picard statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

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

Download


download.png
github.png
galaxy.png
debian.png
conda.png

Versioning


No version available

Documentation


Picard citations

 (2912)
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

[…] n a chromosome were annotated as SGCs. Because homologous TLs, BIRs, and SGCs represent homologous rearrangements, approximate rearrangement positions were notated. Small variants were detected using Picard and GATK. SNVs and InDels reported in AT-rich regions, rDNA regions, telomeres, and regions with too low-coverage (<50% of the average coverage) and that are often seen especially around the la […]

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

[…] a) 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 all -c […]

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

[…] 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 th […]

library_books

Genomic alterations of ground glass nodular lung adenocarcinoma

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

[…] 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 was b […]

call_split

Case Report: Identification of an HNF1B p.Arg527Gln mutation in a Maltese patient with atypical early onset diabetes and diabetic nephropathy

2018
PMCID: 5952643
PMID: 29764441
DOI: 10.1186/s12902-018-0257-z
call_split See protocol

[…] CASAVA. The sequence reads were mapped and aligned to the Human Reference Genome (UCSC hg19, NCBI build 37) using the Burrows-Wheeler transformation algorithm, and duplicated reads were removed using Picard [, ]. FastQC was used to check the quality of sequence data []. Calling of SNPs and InDels was done using GATK Unified Genotyper, which uses a Bayesian genotype likelihood model to report allel […]

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

[…] 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 Har […]

Citations

Looking to check out a full list of citations?

Picard institution(s)
Broad Institute, MA, USA

Picard review

star_border star_border star_border star_border star_border
star star star star star

Arup Ghosh

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