Picard protocols

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Picard statistics

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

 (737)
2018
PMCID: 5753478
PMID: 29298683
DOI: 10.1186/s12864-017-4386-y

[…] (https://github.com/dieterich-lab/dcc) was used to quantify host gene read counts. in accordance with the dcc pipeline, fastq files were mapped with star 2.5 [] using the recommended parameters. picard 2.2.4 (http://broadinstitute.github.io/picard/) was used to remove duplicated reads from the bam files. the circrna raw read counts (using an annotation list of circrnas meeting a 6 read […]

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

[…] was performed as previously described. 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: 5756397
PMID: 29304727
DOI: 10.1186/s12864-017-4416-9

[…] with 20x target coverage. the sequence reads were aligned to the chicken reference genome (galgal4) [] using burrows-wheeler alignment algorithm implemented in bwa [] and sorted using samtools []. picard tools were used to mark duplicates and gatk was used for calling the snps [, ]. for more details on the preparation pipeline see reimer et al. []., the initial array data set contained 918 […]

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: 5761948
PMID: 29320567
DOI: 10.1371/journal.pone.0190987

[…] al.[]. gene expression levels were calculated using the htseq software (http://www-huber.embl.de/users/anders/htseq/; version 0.5.4p3). poor quality reads (phred score < 10) were eliminated using picard tool (http://picard.sourceforge.net/; version 1.83) and only unique reads were considered for gene expression level estimation. the edger method (version 3.2.4), was applied for analysis […]


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Picard in publications

 (3090)
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 […]

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 […]

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 […]

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 […]

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 […]


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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.