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",)