Picard-tools

Introduction

Started as a companion package to GATK (so that GATK could concentrate on its core functions), Picard Tools has blossomed beyond that to be quite substnatial in its own right.

Soem of its functions overlaps with samtools capability.

Its toolbox takes the form of subcommand which are fed to the chief picard-tools program. As it is java, this will be a jar file.

Note that Java 1.8 is a prerequisite for picard-tools.

Usage

picard-tools follows conventions set by GATK. This means that it is a bit awkward clumsy for one-liner command-lines and sits better in a script.

Typical script

Here we use the MergeSamFiles tool.

#!/bin/bash 
A=( $* )
NA=${#A[@]}
INPS=""
for i in ${A[@]}; do
    INPS="$INPS I=$i"
done
INPS="$INPS O=allmerged.bam"
java -jar ~/swmake/jars/picard.jar MergeSamFiles SORT_ORDER=coordinate${INPS}

Note to this: Picard-tools does not have the usual -x <optionvalue> option switches, but rather:

• these is no dash before the option switch
• the option takes an equals sign with no spaces.
• the option switches are in capitals and can also be strings made up of words separated by underscores.

List of all the tools

• AddCommentsToBam
• AddOrReplaceReadGroups
• BaitDesigner
• BamToBfq
• BamIndexStats
• BedToIntervalList
• BuildBamIndex
• CalculateHsMetrics
• CalculateReadGroupChecksum
• CleanSam
• CollectAlignmentSummaryMetrics, only for Illumina data.
• CollectBaseDistributionByCycle
• CollectGcBiasMetrics
• CollectHiSeqXPfFailMetrics
• CollectHsMetrics
• CollectIlluminaBasecallingMetrics
• CollectIlluminaLaneMetrics
• CollectInsertSizeMetrics
• CollectJumpingLibraryMetrics
• CollectMultipleMetrics
• CollectOxoGMetrics
• CollectQualityYieldMetrics
• CollectRawWgsMetrics
• CollectTargetedPcrMetrics
• CollectRnaSeqMetrics
• CollectRrbsMetrics
• CollectSequencingArtifactMetrics
• CollectVariantCallingMetrics
• CollectWgsMetrics
• CollectWgsMetricsFromQuerySorted
• CollectWgsMetricsFromSampledSites
• CollectWgsMetricsWithNonZeroCoverage
• CompareMetrics
• CompareSAMs
• ConvertSequencingArtifactToOxoG
• CreateSequenceDictionary
• DownsampleSam
• ExtractIlluminaBarcodes
• EstimateLibraryComplexity
• FastqToSam
• FifoBuffer
• FindMendelianViolations
• FilterSamReads
• FilterVcf
• FixMateInformation
• GatherBamFiles
• GatherVcfs
• GenotypeConcordance
• IlluminaBasecallsToFastq
• IlluminaBasecallsToSam
• CheckIlluminaDirectory
• CheckTerminatorBlock
• IntervalListTools
• LiftOverIntervalList
• LiftoverVcf
• MakeSitesOnlyVcf
• MarkDuplicates, this is the most widely used tool, often performed after the alignment of reads to the reference.
• MarkDuplicatesWithMateCigar
• MeanQualityByCycle
• MergeBamAlignment
• MergeSamFiles
• MergeVcfs
• NormalizeFasta
• PositionBasedDownsampleSam
• ExtractSequences
• QualityScoreDistribution
• RenameSampleInVcf
• ReorderSam
• ReplaceSamHeader
• RevertSam
• RevertOriginalBaseQualitiesAndAddMateCigar
• SamFormatConverter
• SamToFastq
• ScatterIntervalsByNs
• SetNmMdAndUqTags
• SortSam
• SortVcf
• SplitSamByLibrary
• UmiAwareMarkDuplicatesWithMateCigar
• UpdateVcfSequenceDictionary
• VcfFormatConverter
• MarkIlluminaAdapters
• SplitVcfs
• ValidateSamFile
• ViewSam
• VcfToIntervalList