SYNOPSIS
picard-tools COMMAND [OPTION]...DESCRIPTION
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
BuildBamIndex
CalculateHsMetrics
CleanSam
CollectAlignmentSummaryMetrics
CollectGcBiasMetrics
CollectInsertSizeMetrics
CompareSAMs
CreateSequenceDictionary
EstimateLibraryComplexity
FastqToSam
FixMateInformation
MarkDuplicates
MeanQualityByCycle
MergeBamAlignment
MergeSamFiles
NormalizeFasta
QualityScoreDistribution
ReplaceSamHeader
RevertSam
SamFormatConverter
SamToFastq
SortSam
ValidateSamFile
ViewSam