How To Install picard-tools on Debian 10

Learn how to install picard-tools on Debian 10 with this tutorial. picard-tools is Command line tools to manipulate SAM and BAM files

Introduction

In this tutorial we learn how to install picard-tools on Debian 10.

What is picard-tools

picard-tools is:

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. Picard Tools includes these utilities to manipulate SAM and BAM files: AddCommentsToBam FifoBuffer AddOrReplaceReadGroups FilterSamReads BaitDesigner FilterVcf BamIndexStats FixMateInformation BamToBfq GatherBamFiles BedToIntervalList GatherVcfs BuildBamIndex GenotypeConcordance CalculateHsMetrics IlluminaBasecallsToFastq CalculateReadGroupChecksum IlluminaBasecallsToSam CheckIlluminaDirectory LiftOverIntervalList CheckTerminatorBlock LiftoverVcf CleanSam MakeSitesOnlyVcf CollectAlignmentSummaryMetrics MarkDuplicates CollectBaseDistributionByCycle MarkDuplicatesWithMateCigar CollectGcBiasMetrics MarkIlluminaAdapters CollectHiSeqXPfFailMetrics MeanQualityByCycle CollectIlluminaBasecallingMetrics MergeBamAlignment CollectIlluminaLaneMetrics MergeSamFiles CollectInsertSizeMetrics MergeVcfs CollectJumpingLibraryMetrics NormalizeFasta CollectMultipleMetrics PositionBasedDownsampleSam CollectOxoGMetrics QualityScoreDistribution CollectQualityYieldMetrics RenameSampleInVcf CollectRawWgsMetrics ReorderSam CollectRnaSeqMetrics ReplaceSamHeader CollectRrbsMetrics RevertOriginalBaseQualitiesAndAddMateCigar CollectSequencingArtifactMetrics RevertSam CollectTargetedPcrMetrics SamFormatConverter CollectVariantCallingMetrics SamToFastq CollectWgsMetrics ScatterIntervalsByNs CompareMetrics SortSam CompareSAMs SortVcf ConvertSequencingArtifactToOxoG SplitSamByLibrary CreateSequenceDictionary SplitVcfs DownsampleSam UpdateVcfSequenceDictionary EstimateLibraryComplexity ValidateSamFile ExtractIlluminaBarcodes VcfFormatConverter ExtractSequences VcfToIntervalList FastqToSam ViewSam

There are three methods to install picard-tools on Debian 10. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.

Install picard-tools Using apt-get

Update apt database with apt-get using the following command.

sudo apt-get update

After updating apt database, We can install picard-tools using apt-get by running the following command:

sudo apt-get -y install picard-tools

Install picard-tools Using apt

Update apt database with apt using the following command.

sudo apt update

After updating apt database, We can install picard-tools using apt by running the following command:

sudo apt -y install picard-tools

Install picard-tools Using aptitude

If you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Debian. Update apt database with aptitude using the following command.

sudo aptitude update

After updating apt database, We can install picard-tools using aptitude by running the following command:

sudo aptitude -y install picard-tools

How To Uninstall picard-tools on Debian 10

To uninstall only the picard-tools package we can use the following command:

sudo apt-get remove picard-tools

Uninstall picard-tools And Its Dependencies

To uninstall picard-tools and its dependencies that are no longer needed by Debian 10, we can use the command below:

sudo apt-get -y autoremove picard-tools

Remove picard-tools Configurations and Data

To remove picard-tools configuration and data from Debian 10 we can use the following command:

sudo apt-get -y purge picard-tools

Remove picard-tools configuration, data, and all of its dependencies

We can use the following command to remove picard-tools configurations, data and all of its dependencies, we can use the following command:

sudo apt-get -y autoremove --purge picard-tools

Dependencies

picard-tools have the following dependencies:

References

Summary

In this tutorial we learn how to install picard-tools package on Debian 10 using different package management tools: apt, apt-get and aptitude.