sambamba

tools for working with SAM/BAM data
  https://github.com/lomereiter/sambamba
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Sambamba positions itself as a performant alternative to samtools and provides tools for * Powerful filtering with sambamba view --filter * Picard-like SAM header merging in the merge tool * Optional for operations on whole BAMs * Fast copying of a region to a new file with the slice tool * Duplicate marking/removal, using the Picard criteria