addRG

This function is used for adding read group info for BAM file.

Note

This function is calling gatk’s AddOrReplaceReadGroups function.

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

addRG(bamInput=None, outputdir=None, Xmx="4G",
      stepNum=None, threads=1, upstream=None,
      verbose=False)

  • bamInput: list, input bam files.

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

  • Xmx: str, Xmx mem, default is “4g”.

  • threads: int, how many thread to use, using multiRun to excute.

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

  • upstream: upstream output results(rmduplicate / deduplicate_bismark / bamsort / bismark), used for pipeline. This parameter can be True, which means a new pipeline start.

Example usage:

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

addRG(bamInput=bams, Xmx="4G")