Package: picard-tools (1.46-1)

[ Source: picard-tools  ]

Command line tools to manipulate SAM and BAM files

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: BamToBfq IlluminaBasecallsToSam BuildBamIndex MarkDuplicates CalculateHsMetrics MeanQualityByCycle CleanSam MergeBamAlignment CollectAlignmentSummaryMetrics MergeSamFiles CollectGcBiasMetrics NormalizeFasta CollectInsertSizeMetrics QualityScoreDistribution CollectRnaSeqMetrics ReplaceSamHeader CompareSAMs RevertSam CreateSequenceDictionary SamFormatConverter ExtractIlluminaBarcodes SamToFastq EstimateLibraryComplexity SortSam FastqToSam ValidateSamFile FixMateInformation ViewSam

Other Packages Related to picard-tools

• dep: libsam-java (>= 1.46-1)

  Java library to manipulate SAM and BAM files

• dep: openjdk-6-jre

  OpenJDK Java runtime, using Hotspot JIT

  or java-runtime

  virtual package provided by default-jre, gcj-4.6-jre, gcj-4.7-jre, gcj-jre, openjdk-6-jre, openjdk-7-jre

• sug: python

  interactive high-level object-oriented language (default version)

• sug: r-base-core

  GNU R core of statistical computation and graphics system

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