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
- C++ compiler (gcc >= 5.4.0)
- samtools >= 1.3 or sambamba >= 0.6.6
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" >> ~/.bashrcfast-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 |