pileup2seqz: generate.seqz

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run sequenza-utils.py in sequenza (pileup2seqz, seqz-binning)

Usage

pileup2seqz(gc.fn, normal.pileup.gz, window=1000000, tumor.pileup.gz, output.dir, run.cmd=T, mc.cores=1)

Arguments

normal.pileup.gz	samtools pileup file of normal sample
window	A parameter value for -w in sequenza. Indicate a window size (in bases), to be used for the binning.
tumor.pileup.gz	samtools pileup file of tumor sample
fn.gc	output file of generate.GC function

Details

A seqz file contains genotype information, alleles and mutation frequency, and other features. This file is used as input for the R-based part of Sequenza.

References

Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data.

See Also

https://cran.r-project.org/web/packages/sequenza/vignettes/sequenza.pdf

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.