Picard-Teaching
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Category
Bioinformatics
Program On
Teaching
Version
2.16.0
Author / Distributor
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
Installation
Source code is obtained from picard
System
64-bit Linux