Picard-Teaching

Category

Bioinformatics

Program On

Teaching

Version

2.16.0

Author / Distributor

picard

Description

"A set of tools (in Java) for working with next generation sequencing data in the BAM format." More details are at picard

Running Program

The last version of this application is at /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144

To use this version, please load the module with

ml picard/2.16.0-Java-1.8.0_144 

Here is an example of a shell script, sub.sh, to run on the batch queue:

#!/bin/bash
#SBATCH --job-name=j_picard
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=picard.%j.out
#SBATCH --error=picard.%j.err

cd $SLURM_SUBMIT_DIR
ml picard/2.16.0-Java-1.8.0_144
java -jar /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar [options]

In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.

Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.

Here is an example of job submission command:

sbatch ./sub.sh 

Documentation

ml picard/2.16.0-Java-1.8.0_144 
java -jar /usr/local/apps/eb/picard/2.16.0-Java-1.8.0_144/picard.jar -h
�[1m�[31mUSAGE: PicardCommandLine �[32m<program name>�[1m�[31m [-h]

�[0m�[1m�[31mAvailable Programs:
�[0m�[37m--------------------------------------------------------------------------------------
�[0m�[31mAlpha Tools:                                     Tools that are currently UNSUPPORTED until further testing and maturation.�[0m
�[32m    CollectIndependentReplicateMetrics           �[36m(Experimental) Estimates the rate of independent replication of reads within a bam.�[0m
�[32m    CollectWgsMetricsWithNonZeroCoverage         �[36m(Experimental) Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments.  �[0m
�[32m    UmiAwareMarkDuplicatesWithMateCigar          �[36mIdentifies duplicate reads using information from read positions and UMIs. �[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mFasta:                                           Tools for manipulating FASTA, or related data.�[0m
�[32m    CreateSequenceDictionary                     �[36mCreates a sequence dictionary for a reference sequence.  �[0m
�[32m    ExtractSequences                             �[36mSubsets intervals from a reference sequence to a new FASTA file.�[0m
�[32m    NonNFastaSize                                �[36mCounts the number of non-N bases in a fasta file.�[0m
�[32m    NormalizeFasta                               �[36mNormalizes lines of sequence in a FASTA file to be of the same length.�[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mFingerprinting Tools:                            Tools for manipulating fingerprints, or related data.�[0m
�[32m    CheckFingerprint                             �[36mComputes a fingerprint from the supplied input (SAM/BAM or VCF) file and compares it to the provided genotypes�[0m
�[32m    ClusterCrosscheckMetrics                     �[36mClusters the results of a CrosscheckFingerprints run by LOD score.�[0m
�[32m    CrosscheckFingerprints                       �[36mChecks if all fingerprints appear to come from the same individual.�[0m
�[32m    CrosscheckReadGroupFingerprints              �[36mDEPRECATED: USE CrosscheckFingerprints. Checks if all read groups appear to come from the same individual.�[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mIllumina Tools:                                  Tools for manipulating data specific to Illumina sequencers.�[0m
�[32m    CheckIlluminaDirectory                       �[36mAsserts the validity for specified Illumina basecalling data.  �[0m
�[32m    CollectIlluminaBasecallingMetrics            �[36mCollects Illumina Basecalling metrics for a sequencing run.  �[0m
�[32m    CollectIlluminaLaneMetrics                   �[36mCollects Illumina lane metrics for the given BaseCalling analysis directory.  �[0m
�[32m    ExtractIlluminaBarcodes                      �[36mTool determines the barcode for each read in an Illumina lane.  �[0m
�[32m    IlluminaBasecallsToFastq                     �[36mGenerate FASTQ file(s) from Illumina basecall read data.  �[0m
�[32m    IlluminaBasecallsToSam                       �[36mTransforms raw Illumina sequencing data into an unmapped SAM or BAM file.�[0m
�[32m    MarkIlluminaAdapters                         �[36mReads a SAM or BAM file and rewrites it with new adapter-trimming tags.  �[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mInterval Tools:                                  Tools for manipulating Picard interval lists.�[0m
�[32m    BedToIntervalList                            �[36mConverts a BED file to a Picard Interval List.  �[0m
�[32m    IntervalListToBed                            �[36mConverts an Picard IntervalList file to a BED file.�[0m
�[32m    IntervalListTools                            �[36mManipulates interval lists.  �[0m
�[32m    LiftOverIntervalList                         �[36mLifts over an interval list from one reference build to another.  �[0m
�[32m    ScatterIntervalsByNs                         �[36mWrites an interval list based on splitting a reference by Ns.  �[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mMetrics:                                         Tools for reporting metrics on various data types.�[0m
�[32m    AccumulateVariantCallingMetrics              �[36mCombines multiple Variant Calling Metrics files into a single file�[0m
�[32m    CollectAlignmentSummaryMetrics               �[36m<b>Produces a summary of alignment metrics from a SAM or BAM file.</b>  �[0m
�[32m    CollectBaseDistributionByCycle               �[36mChart the nucleotide distribution per cycle in a SAM or BAM file�[0m
�[32m    CollectGcBiasMetrics                         �[36mCollect metrics regarding GC bias. �[0m
�[32m    CollectHiSeqXPfFailMetrics                   �[36mClassify PF-Failing reads in a HiSeqX Illumina Basecalling directory into various categories.�[0m
�[32m    CollectHsMetrics                             �[36mCollects hybrid-selection (HS) metrics for a SAM or BAM file.  �[0m
�[32m    CollectInsertSizeMetrics                     �[36mCollect metrics about the insert size distribution of a paired-end library.�[0m
�[32m    CollectJumpingLibraryMetrics                 �[36mCollect jumping library metrics. �[0m
�[32m    CollectMultipleMetrics                       �[36mCollect multiple classes of metrics.  �[0m
�[32m    CollectOxoGMetrics                           �[36mCollect metrics to assess oxidative artifacts.�[0m
�[32m    CollectQualityYieldMetrics                   �[36mCollect metrics about reads that pass quality thresholds and Illumina-specific filters.  �[0m
�[32m    CollectRawWgsMetrics                         �[36mCollect whole genome sequencing-related metrics.  �[0m
�[32m    CollectRnaSeqMetrics                         �[36mProduces RNA alignment metrics for a SAM or BAM file.  �[0m
�[32m    CollectRrbsMetrics                           �[36m<b>Collects metrics from reduced representation bisulfite sequencing (Rrbs) data.</b>  �[0m
�[32m    CollectSequencingArtifactMetrics             �[36mCollect metrics to quantify single-base sequencing artifacts.  �[0m
�[32m    CollectTargetedPcrMetrics                    �[36mCalculate PCR-related metrics from targeted sequencing data. �[0m
�[32m    CollectVariantCallingMetrics                 �[36mCollects per-sample and aggregate (spanning all samples) metrics from the provided VCF file�[0m
�[32m    CollectWgsMetrics                            �[36mCollect metrics about coverage and performance of whole genome sequencing (WGS) experiments.�[0m
�[32m    CompareMetrics                               �[36mCompare two metrics files.�[0m
�[32m    ConvertSequencingArtifactToOxoG              �[36mExtract OxoG metrics from generalized artifacts metrics.  �[0m
�[32m    EstimateLibraryComplexity                    �[36mEstimates the numbers of unique molecules in a sequencing library.  �[0m
�[32m    MeanQualityByCycle                           �[36mCollect mean quality by cycle.�[0m
�[32m    QualityScoreDistribution                     �[36mChart the distribution of quality scores.  �[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mMiscellaneous Tools:                             A set of miscellaneous tools.                �[0m
�[32m    BaitDesigner                                 �[36mDesigns oligonucleotide baits for hybrid selection reactions.�[0m
�[32m    FifoBuffer                                   �[36mFIFO buffer used to buffer input and output streams with a customizable buffer size �[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mSAM/BAM:                                         Tools for manipulating SAM, BAM, or related data.�[0m
�[32m    AddCommentsToBam                             �[36mAdds comments to the header of a BAM file.�[0m
�[32m    AddOrReplaceReadGroups                       �[36mReplace read groups in a BAM file.�[0m
�[32m    BamIndexStats                                �[36mGenerate index statistics from a BAM file�[0m
�[32m    BamToBfq                                     �[36mCreate BFQ files from a BAM file for use by the maq aligner.  �[0m
�[32m    BuildBamIndex                                �[36mGenerates a BAM index ".bai" file.  �[0m
�[32m    CalculateReadGroupChecksum                   �[36mCreates a hash code based on the read groups (RG).  �[0m
�[32m    CheckTerminatorBlock                         �[36mAsserts the provided gzip file's (e.g., BAM) last block is well-formed; RC 100 otherwise�[0m
�[32m    CleanSam                                     �[36mCleans the provided SAM/BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads�[0m
�[32m    CompareSAMs                                  �[36mCompare two input ".sam" or ".bam" files.  �[0m
�[32m    DownsampleSam                                �[36mDownsample a SAM or BAM file.  �[0m
�[32m    FastqToSam                                   �[36mConverts a FASTQ file to an unaligned BAM or SAM file.  �[0m
�[32m    FilterSamReads                               �[36mSubset read data from a SAM or BAM file�[0m
�[32m    FixMateInformation                           �[36mVerify mate-pair information between mates and fix if needed.�[0m
�[32m    GatherBamFiles                               �[36mConcatenate one or more BAM files as efficiently as possible�[0m
�[32m    MarkDuplicates                               �[36mIdentifies duplicate reads.  �[0m
�[32m    MarkDuplicatesWithMateCigar                  �[36mIdentifies duplicate reads, accounting for mate CIGAR.  �[0m
�[32m    MergeBamAlignment                            �[36mMerge alignment data from a SAM or BAM with data in an unmapped BAM file.  �[0m
�[32m    MergeSamFiles                                �[36mMerges multiple SAM and/or BAM files into a single file.  �[0m
�[32m    PositionBasedDownsampleSam                   �[36mDownsample a SAM or BAM file to retain a subset of the reads based on the reads location in each tile in the flowcell.�[0m
�[32m    ReorderSam                                   �[36mReorders reads in a SAM or BAM file to match ordering in reference�[0m
�[32m    ReplaceSamHeader                             �[36mReplaces the SAMFileHeader in a SAM or BAM file.  �[0m
�[32m    RevertOriginalBaseQualitiesAndAddMateCigar   �[36mReverts the original base qualities and adds the mate cigar tag to read-group BAMs�[0m
�[32m    RevertSam                                    �[36mReverts SAM or BAM files to a previous state.  �[0m
�[32m    SamFormatConverter                           �[36mConvert a BAM file to a SAM file, or a SAM to a BAM�[0m
�[32m    SamToFastq                                   �[36mConverts a SAM or BAM file to FASTQ.  �[0m
�[32m    SetNmAndUqTags                               �[36mDEPRECATED: Use SetNmMdAndUqTags instead.�[0m
�[32m    SetNmMdAndUqTags                             �[36mFixes the NM, MD, and UQ tags in a SAM file.  �[0m
�[32m    SortSam                                      �[36mSorts a SAM or BAM file.  �[0m
�[32m    SplitSamByLibrary                            �[36mSplits a SAM or BAM file into individual files by library�[0m
�[32m    SplitSamByNumberOfReads                      �[36mSplits a SAM or BAM file to multiple BAMs.�[0m
�[32m    ValidateSamFile                              �[36mValidates a SAM or BAM file.  �[0m
�[32m    ViewSam                                      �[36mPrints a SAM or BAM file to the screen�[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mUnit Testing:                                    Unit testing                                 �[0m
�[32m    SimpleMarkDuplicatesWithMateCigar            �[36m(Experimental) Examines aligned records in the supplied SAM or BAM file to locate duplicate molecules.�[0m

�[37m--------------------------------------------------------------------------------------
�[0m�[31mVCF/BCF:                                         Tools for manipulating VCF, BCF, or related data.�[0m
�[32m    FilterVcf                                    �[36mHard filters a VCF.�[0m
�[32m    FindMendelianViolations                      �[36mFinds mendelian violations of all types within a VCF�[0m
�[32m    FixVcfHeader                                 �[36mReplaces or fixes a VCF header.�[0m
�[32m    GatherVcfs                                   �[36mGathers multiple VCF files from a scatter operation into a single VCF file�[0m
�[32m    GenotypeConcordance                          �[36mEvaluate genotype concordance between callsets.�[0m
�[32m    LiftoverVcf                                  �[36mLifts over a VCF file from one reference build to another.  �[0m
�[32m    MakeSitesOnlyVcf                             �[36mCreates a VCF bereft of genotype information from an input VCF or BCF�[0m
�[32m    MergeVcfs                                    �[36mMerges multiple VCF or BCF files into one VCF file or BCF�[0m
�[32m    RenameSampleInVcf                            �[36mRenames a sample within a VCF or BCF.  �[0m
�[32m    SortVcf                                      �[36mSorts one or more VCF files.  �[0m
�[32m    SplitVcfs                                    �[36mSplits SNPs and INDELs into separate files.  �[0m
�[32m    UpdateVcfSequenceDictionary                  �[36mTakes a VCF and a second file that contains a sequence dictionary and updates the VCF with the new sequence dictionary.�[0m
�[32m    VcfFormatConverter                           �[36mConverts VCF to BCF or BCF to VCF.  �[0m
�[32m    VcfToIntervalList                            �[36mConverts a VCF or BCF file to a Picard Interval List.�[0m

�[37m--------------------------------------------------------------------------------------

�[0m

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Installation

Source code is obtained from picard

System

64-bit Linux