Manipulate sam and bam files
picard-tools COMMAND [OPTION]...
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: AddOrReplaceReadGroups BamToBfq BamIndexStats BuildBamIndex CalculateHsMetrics CleanSam CollectAlignmentSummaryMetrics CollectGcBiasMetrics CollectInsertSizeMetrics CollectMultipleMetrics CollectTargetedPcrMetrics CollectRnaSeqMetrics CompareSAMs CreateSequenceDictionary DownsampleSam ExtractIlluminaBarcodes EstimateLibraryComplexity FastqToSam FilterSamReads FixMateInformation IlluminaBasecallsToFastq IlluminaBasecallsToSam CheckIlluminaDirectory IntervalListTools MarkDuplicates MeanQualityByCycle MergeBamAlignment MergeSamFiles MergeVcfs NormalizeFasta ExtractSequences QualityScoreDistribution ReorderSam ReplaceSamHeader RevertSam SamFormatConverter SamToFastq SortSam VcfFormatConverter SplitVcfs ValidateSamFile ViewSam
Copyright 2010 The Broad Institute
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