bamsort

This function is used for sorting bam files.

Note

This function is calling samtools.

samtools official docs

Li, Heng, et al. “The sequence alignment/map format and SAMtools.” Bioinformatics 25.16 (2009): 2078-2079.

Parameters

bamsort(bamInput=None, outputdir=None,
        threads=1, stepNum=None, upstream=None)

  • bamInput: list, bam file input.

  • outputdir: str, output result folder, None means the same folder as input files.

  • threads: int, how many thread to use.

  • stepNum: int or str, step flag for folder name.

  • upstream: upstream output results, used for pipeline.

  • verbose: bool, True means print all stdout, but will be slow; False means black stdout verbose, much faster.

Example usage:

bams = ["test1.bam", "test1.bam"]

bamsort(bamInput=bams)