qualimap

This function is for bam file statistics, generating the coverage, depth, map ratio in each chromosome, some figures and so on.

Note

Note: this function is calling qualimap, please install qualimap before using.

qualimap official docs

Okonechnikov, Konstantin, Ana Conesa, and Fernando García-Alcalde. “Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data.” Bioinformatics 32.2 (2016): 292-294.

Parameters

qualimap(bamInput=None, outputdir=None, memSize="8G",
         stepNum=None, upstream=None, threads=1,
         verbose=False, other_params=None, **kwargs)

  • bamInput: list, Input bam files.

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

  • memSize: str, mem size for java, default is 8G.

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

  • upstream: upstream output results, used for pipeline. This parameter can be True, which means a new pipeline start.

  • other_params: dict or str, other_params for qualimap, eg: for panel data, you can set {“–gff”:’xx.bed’} for target region analysis.

  • threads: int, how many threads used?

  • 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"]

qualimap(bamInput=bams)