cfDNAWGS

This function is used for processing paired/single end WGS data.

Note

User must set Configure or pipeConfigure before using. This function provides basic processing steps, like alignment and bis correction. If you want to perform comparison process, please use cfDNAWGBS2.

Parameters

cfDNAWGBS(inputFolder=None, fastq1=None, fastq2=None,
          adapter1=["AGATCGGAAGAGCACACGTCTGAACTCCAGTCA"],
          adapter2=["AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"],
          fastqcOP=None,
          idAdapter=True,
          idAdOP=None,
          rmAdapter=True,
          rmAdOP={"--qualitybase": 33, "--gzip": True},
          bismarkOP={"-q": True, "--phred33-quals": True, "--bowtie2": True, "--un": True,},
          dudup=True,
          dudupOP=None,
          extractMethyOP={
              "--no_overlap": True,
              "--report": True,
              "--no_header": True,
              "--gzip": True,
              "--bedGraph": True,
              "--zero_based": True,
              },
          methyRegion=None,
          CNV=False,
          fragProfile=False,
          deconvolution=False,
          report=False,
          verbose=False,
          box=True)

  • inputFolder: str, input fastq file folder path. Setting this parameter means disable fastq1 and fastq2.

  • fastq1: list, fastq1 files.

  • fastq2: list, fastq2 files.

  • adapter1: list, adapters for fastq1 files, if idAdapter is True, this paramter will be disabled.

  • adapter2: list, adapters for fastq2 files, if idAdapter is True, this paramter will be disabled.

  • fastqcOP: Other parameters used for fastqc, please see class “fastqc”.

  • idAdapter: Ture or False, identify adapters or not. This module is not for single end data.

  • idAdOP: Other parameters used for AdapterRemoval, please see class “identifyAdapter”.

    If idAdapter is False, this paramter will be disabled.

  • rmAdapter: Ture or False, remove adapters or not.

  • rmAdOP: Other parameters used for AdapterRemoval, please see class “adapterremoval”.

    Default: {“–qualitybase”: 33, “–gzip”: True}. If rmAdapter is False, this paramter will be disabled.

  • bismarkOP: Other parameters used for Bismark, please see class “bismark”.

    Default: {“-q”: True, “–phred33-quals”: True, “–bowtie2”: True, “–un”: True,}.

  • dudup: Ture or False, remove duplicates for bismark results or not.

  • dudupOP: Other parameters used for bismark_deduplicate, please see class “bismark_deduplicate”.

    If dudup is False, this paramter will be disabled.

  • extractMethyOP: Other parameters used for bismark_methylation_extractor, please see class “bismark_methylation_extractor”.
    Default: {“–no_overlap”: True, “–report”: True, “–no_header”: True, “–gzip”: True,

    “–bedGraph”: True, “–zero_based”: True,}

  • methyRegion: Bed file contains methylation related regions.

  • CNV: Compute basic CNV or not.

  • armCNV: Compute basic arm level CNV related values. The arm level cnv detection needs control/healthy samples,

    therefore only operating function “cfDNAWGS” will get no results in report. This function is designed for case control study in function cfDNAWGS2.

  • fragProfile: Compute basic fragProfile (long short fragement statistics) related values. This module is not for single end data.

    The fragProfile detection needs control/healthy samples, therefore only operating function “cfDNAWGS” will get no results in report. This function is designed for case control study in function cfDNAWGS2.

  • deconvolution: Compute tissue proportion for each sample or not.

  • report: Generate user report or not.

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

  • box: output will be a box class. that mean the the results can be specified using ‘.’,

    otherwise, the results will be saved as dict.

Example usage:

from cfDNApipe import *

pipeConfigure(
    threads=60,
    genome="hg19",
    refdir=r"path_to_genome/hg19_bismark",
        outdir=r"path_to_output/output",
    data="WGBS",
    type="paired",
    build=True,
    JavaMem="10g",
)

res = cfDNAWGBS(
    inputFolder=r"path_to_fastqs",
    idAdapter=True,
    rmAdapter=True,
    dudup=True,
    CNV=True,
    armCNV=True,
    fragProfile=True,
    report=True,
    verbose=False,
)