Picard-tools - Revision history

Rf at 14:51, 9 March 2017

2017-03-09T14:51:00Z

Rf at 14:49, 9 March 2017

2017-03-09T14:49:55Z

Rf at 14:47, 9 March 2017

2017-03-09T14:47:28Z

Rf at 14:37, 9 March 2017

2017-03-09T14:37:15Z

Rf at 18:40, 15 February 2017

2017-02-15T18:40:36Z

Rf at 18:39, 15 February 2017

2017-02-15T18:39:59Z

Rf: Created page with "= Introduction = Started as a companion package to GATK, so that GATK could concentrate on its core functions, but has blossomed beyond that to be quite substnatial in its ow..."

2017-02-15T18:22:04Z

Created page with "= Introduction = Started as a companion package to GATK, so that GATK could concentrate on its core functions, but has blossomed beyond that to be quite substnatial in its ow..."

New page

= Introduction =

Started as a companion package to GATK, so that GATK could concentrate on its core functions, but has blossomed beyond that to be quite substnatial in its own right, and is sometimes better than samtools.

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}

@@ Line 44: / Line 44: @@
 * CalculateReadGroupChecksum
 * CleanSam
-* CollectAlignmentSummaryMetrics, only for Illumina data.
+* '''CollectAlignmentSummaryMetrics''', only for Illumina data.
 * CollectBaseDistributionByCycle
 * CollectGcBiasMetrics
@@ Line 90: / Line 90: @@
 * LiftoverVcf
 * MakeSitesOnlyVcf
-* MarkDuplicates
+* '''MarkDuplicates''', this is the most widely used tool, often performed after the alignment of reads to the reference.
 * MarkDuplicatesWithMateCigar
 * MeanQualityByCycle

@@ Line 44: / Line 44: @@
 * CalculateReadGroupChecksum
 * CleanSam
-* CollectAlignmentSummaryMetrics
+* CollectAlignmentSummaryMetrics, only for Illumina data.
 * CollectBaseDistributionByCycle
 * CollectGcBiasMetrics

← Older revision		Revision as of 14:47, 9 March 2017
Line 31:		Line 31:
	* the option takes an equals sign with no spaces.		* 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.		* 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
		+	* 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
		+	* 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

@@ Line 24: / Line 24: @@
   java -jar ~/swmake/jars/picard.jar MergeSamFiles SORT_ORDER=coordinate${INPS}
-<ins>This to note</ins>:
+<ins>Note to this</ins>:
-picard-tools does n't have the usual '''-x <optionvalue>''' option switches, but rather:
+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.

@@ Line 1: / Line 1: @@
 = Introduction =
-Started as a companion package to GATK, so that GATK could concentrate on its core functions, but has blossomed beyond that to be quite substnatial in its own right, and is sometimes better than samtools.
+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.
 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.

@@ Line 19: / Line 19: @@
   INPS=""
   for i in ${A[@]}; do
-      INPS="$INPS -I $i"
+      INPS="$INPS I=$i"
   done
-  INPS="$INPS -O allmerged.bam"
+  INPS="$INPS O=allmerged.bam"
   java -jar ~/swmake/jars/picard.jar MergeSamFiles SORT_ORDER=coordinate${INPS}