Picard pipeline

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 IN pipelines

 (591)
2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] was performed as previously described34. briefly, the burrows-wheeler aligner (bwa-mem, version 0.7.7) was used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). […]

2018
PMCID: 5754367
PMID: 29302025
DOI: 10.1038/s41467-017-02306-5

[…] described34. briefly, the burrows-wheeler aligner (bwa-mem, version 0.7.7) was used to map all reads to ucsc hg19. pcr duplicates were removed from alignments using picard version 1.96 (http://picard.sourceforge.net). indels were realigned using the genome analysis toolkit (gatk). snvs and short indels were called using gatk haplotype caller (version 3.4–46). all variants were annotated […]

2018
PMCID: 5757203
PMID: 29379323
DOI: 10.2147/LCTT.S147841

[…] depth using illumina (san diego, ca, usa) hiseq 2500® instrument., the raw fastq sequences obtained were aligned to human reference genome (grch37/hg19) using bwa program32,33 and processed using picard and gatk toolkits.34,35 the low frequency variants were identified using lofreq program. an in-house method has been developed to filter the low frequency variant to control false positive […]

2018
PMCID: 5760544
PMID: 29317692
DOI: 10.1038/s41598-017-18358-y

[…] to paired-end 101-bp sequencing on an illumina hiseq 2500 platform (san diego, ca, usa)., paired-end reads were mapped against the human reference genome (hg19, grch37) using bwa software (0.7.12). picard tools were used to remove pcr-duplicated and multiple aligned reads. after filtering out low-quality reads with mapping quality < 13 and base quality < 13, snp calling was performed […]

2018
PMCID: 5763955
PMID: 29321057
DOI: 10.1186/s40168-017-0386-z

[…] using the truseq sbs hs v3 chemistry on an illumina hiseq 2500 sequencer. quality control (qc) was done with fastqc v.0.11.5. reads were mapped with tophat2 v.2.0.11. biological qc was done with picardtools v.1.141. reads per gene feature were counted with htseq v.0.6p1. normalization was performed according to the design model with r/bioconductor edger v. 3.4.2. gene ontology analysis […]

Picard institution(s)
Broad Institute, MA, USA

Picard review

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Arup Ghosh

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