Large Scale CNV¶
The Following example shows how to perform large scale CNV analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.
CNV Example usage¶
from cfDNApipe import *
import glob
pipeConfigure2(
threads=20,
genome="hg19",
refdir=r"reference_genome/hg19",
outdir=r"output/pcs_armCNV",
data="WGS",
type="paired",
JavaMem="8G",
case="cancer",
ctrl="normal",
build=True,
)
verbose = False
case_bam = glob.glob("path_to_data/HCC/*.bam")
ctrl_bam = glob.glob("path_to_data/CTR/*.bam")
# case
switchConfigure("cancer")
case_bamCounter = bamCounter(
bamInput=case_bam, upstream=True, verbose=verbose, stepNum="case01"
)
case_gcCounter = runCounter(
filetype=0, upstream=True, verbose=verbose, stepNum="case02"
)
case_GCCorrect = GCCorrect(
readupstream=case_bamCounter,
gcupstream=case_gcCounter,
verbose=verbose,
stepNum="case03",
)
# ctrl
switchConfigure("normal")
ctrl_bamCounter = bamCounter(
bamInput=ctrl_bam, upstream=True, verbose=verbose, stepNum="ctrl01"
)
ctrl_gcCounter = runCounter(
filetype=0, upstream=True, verbose=verbose, stepNum="ctrl02"
)
ctrl_GCCorrect = GCCorrect(
readupstream=ctrl_bamCounter,
gcupstream=ctrl_gcCounter,
verbose=verbose,
stepNum="ctrl03",
)
switchConfigure("cancer")
res_computeCNV = computeCNV(
caseupstream=case_GCCorrect,
ctrlupstream=ctrl_GCCorrect,
stepNum="ARMCNV",
verbose=verbose,
)