Bin Scale CNV¶
The Following example shows how to perform bin-scale CNV analysis. For up- and down-stream relationship, please see “Up Down Stream Flowchart” part.
bin-scale CNV Example usage¶
from cfDNApipe import *
pipeConfigure(
threads=20,
genome="hg19",
refdir=r"path_to_reference/hg19_bowtie2",
outdir=r"path_to_output/WGS",
data="WGS",
type="paired",
JavaMem="10G",
build=True,
)
verbose = False
res_inputprocess = inputprocess(inputFolder="path_to_fastq")
res_fastqc = fastqc(upstream=res_inputprocess, verbose=verbose)
res_identifyAdapter = identifyAdapter(upstream=res_inputprocess, verbose=verbose)
res_adapterremoval = adapterremoval(upstream=res_identifyAdapter, verbose=verbose)
res_bowtie2 = bowtie2(upstream=res_adapterremoval, verbose=verbose)
res_bamsort = bamsort(upstream=res_bowtie2, verbose=verbose)
res_rmduplicate = rmduplicate(upstream=res_bamsort, verbose=verbose)
res_cnvbatch = cnvbatch(
caseupstream=res_rmduplicate,
access=Configure.getConfig("access-mappable"),
annotate=Configure.getConfig("refFlat"),
verbose=verbose,
stepNum="CNV01",
)
res_cnvPlot = cnvPlot(upstream=res_cnvbatch, verbose=verbose, stepNum="CNV02",)
res_cnvTable = cnvTable(upstream=res_cnvbatch, verbose=verbose, stepNum="CNV03",)
res_cnvHeatmap = cnvHeatmap(upstream=res_cnvbatch, verbose=verbose, stepNum="CNV04",)