mutect2n

This function is used for Call normal sample’s SNVs and indels via local assembly of haplotypes using gatk.

Note

This function is calling Mutect2. This function is only suit for paired data.

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

mutect2t(bamInput=None, outputdir=None,
    genome=None, ref=None, threads=1,
    stepNum=None, other_params={"-max-mnp-distance": 0},
    upstream=None, verbose=False, **kwargs)

• bamInput: list, bam files, just as Output for next step analysis.

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

• other_params: dict, other parameters for gatk mutect, default is {“-max-mnp-distance”: 0},

• threads: int, how many thread to use.

• genome: str, human genome version, just support “hg19” and “hg38”

• ref: str, reference folderpath.

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

• upstream: upstream output results, used for call snp pipeline, just can be BQSR / addRG. This parameter can be True, which means a new pipeline start.

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

Warning

We recommend using this function in SNV detection. For a detailed tutorial, please see SNV detection tutorial.

Example usage:

from cfDNApipe import *
import glob

# set global configure
pipeConfigure2(
    threads=100,
    genome="hg19",
    refdir=r"path_to_reference/hg19",
    outdir=r"path_to_output/snv_output",
    data="WGS",
    type="paired",
    case="cancer",
    ctrl="normal",
    JavaMem="10g",
    build=True,
)

Configure2.snvRefCheck(folder="path_to_reference/hg19/SNV_hg19", build=True)

case_bams = glob.glob("path_to_samples/cancer/*.bam")
ctrl_bams = glob.glob("path_to_samples/normal/*.bam")

# create PON file from normal samples
switchConfigure("normal")

ctrl_addRG = addRG(bamInput=ctrl_bams, upstream=True, stepNum="PON00",)
ctrl_BaseRecalibrator = BaseRecalibrator(
        upstream=ctrl_addRG,
        knownSitesDir=Configure2.getConfig("snv.folder"),
        stepNum="PON01",
        )
ctrl_BQSR = BQSR(upstream = ctrl_BaseRecalibrator, stepNum="PON02",)
ctrl_mutect2n = mutect2n(upstream = ctrl_BQSR, stepNum="PON03",)
ctrl_dbimport = dbimport(upstream = ctrl_mutect2n, stepNum="PON04",)
ctrl_createPon = createPON(upstream = ctrl_dbimport, stepNum="PON05",)

# performing comparison between cancer and normal
switchConfigure("cancer")
case_addRG = addRG(bamInput=case_bams, upstream=True, stepNum="SNV00",)
case_BaseRecalibrator = BaseRecalibrator(
    upstream=case_addRG,
    knownSitesDir=Configure2.getConfig("snv.folder"),
    stepNum="SNV01",
)

case_BQSR = BQSR(
    upstream=case_BaseRecalibrator,
    stepNum="SNV02")

case_getPileup = getPileup(
    upstream=case_BQSR,
    biallelicvcfInput=Configure2.getConfig('snv.ref')["7"],
    stepNum="SNV03",
)
case_contamination = contamination(
    upstream=case_getPileup,
    stepNum="SNV04"
)

# In this step, ponbedInput is ignored by using caseupstream parameter
case_mutect2t = mutect2t(
    caseupstream=case_contamination,
    ctrlupstream=ctrl_createPon,
    vcfInput=Configure2.getConfig('snv.ref')["6"],
    stepNum="SNV05",
)

case_filterMutectCalls = filterMutectCalls(
    upstream=case_mutect2t,
    stepNum="SNV06"
)

case_gatherVCF = gatherVCF(
    upstream=case_filterMutectCalls,
    stepNum="SNV07"
)

# split somatic mutations
case_somatic = bcftoolsVCF(upstream=case_gatherVCF, stepNum="somatic")

# split germline mutations
case_germline = bcftoolsVCF(
    upstream=case_gatherVCF, other_params={"-f": "'germline'"}, suffix="germline", stepNum="germline"
)