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fast-samtools-sort

fast-samtools-sort is a fast BAM read sorter implemented on top of Samtools or Sambamba. This tool allows for faster sorting of BAM files than the default sorter supplied in Samtools or Sambamba.

Authors: Christopher Bennett Christopher.Bennett@UTSouthwestern.edu and Daehwan Kim infphilo@gmail.com

Installation

Dependencies

  • C++ compiler (gcc >= 5.4.0)
  • samtools >= 1.3 or sambamba >= 0.6.6

Install

For this example you clone fast_samtools_sort into a directory within your user directory called fast-samtools, make the executable, and add the directory to your PATH.

git clone https://github.com/chbe-helix/fast_samtools_sort.git ~/fast-samtools/
cd ~/fast-samtools/

make
echo "export=PATH=~/fast-samtools/:$PATH" >> ~/.bashrc

Usage

fast-samtools-sort [-l complevel] [-m maxMem] [-o out.bam] [-@/--threads threads] [in.bam]

Sort alignments by alignment position in genome.

The sorted output is written to .bam.sorted file, or to the specified file (out.bam) when -o is used.

Options Description
-l INT Compression level from 0 (no compression, fastest) to 9 (highest compression, slowest) (Default: 6?)
-m INT[G/M/K] Maximum memory in total, shared by threads (Default: 2G?)
-o STR Output filename (Default: $file-name.bam.sorted)
-@/--threads INT Number of threads to use (Default: 1)
-v/--verbose Verbose

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Alpha Version of a SAM format sorter - Currently Not operational on large SAMs

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