rmduplicate

This function is used for removing duplicates in WGS data.

Note

This function is calling gatk, please install GATK before using.

gatk official docs

McKenna, Aaron, et al. “The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data.” Genome research 20.9 (2010): 1297-1303.

Parameters

rmduplicate(bamInput=None, outputdir=None,
            threads=1, stepNum=None,
            upstream=None, verbose=True)

  • bamInput: list, bam file input.

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

  • Xmx: How many memory will be used for every thread, default: 4G.

  • 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"]

rmduplicate(bamInput=bams)