sambamba

Version:
0.6.x
Identifier: TL_bf790f.e9
Tool

Description


This tool is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM, BAM and CRAM formats.

Subtools

  • sambamba markdup

    Marks (by default) or removes duplicate reads. For determining whether a read is a duplicate or not, the same criteria as in Picard are used.

  • sambamba slice

    Outputs reads overlapping specified region into new BAM file. (Default destination is STDOUT.) Input file must be coordinate-sorted and indexed. While

  • sambamba flagstat

    Outputs some statistics drawn from read flags. First line contains numbers of QC-passed and QC-failed reads. Then come pairs of numbers, the former fo

  • sambamba index

    sambamba index builds an index for a sorted by coordinate BAM file. This step is required for effective region querying in most tools for working with

  • sambamba merge

    sambamba merge is used for merging several sorted BAM files into one. The sorting order of all the files must be the same, and it is maintained in the

  • sambamba sort

    BAM files can have either 'coordinate' sort order, or 'qname' one. The first one means to sort the file by (integer) reference ID, and for each refere

  • sambamba view

    sambamba view allows to efficiently filter BAM file for alignments satisfying various conditions, as well as access its SAM header and information abo