mutect: A wrapper around somatic mutation caller MuTect

In flow-r/ngsflows: Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr

Description

This generates a set of commandlines, per chromosome

Usage

mutect(tumor_bam, normal_bam, samplename = opts_flow$get("samplename"),
  outfile, is_merged = TRUE, split_by_chr = TRUE,
  java_exe = opts_flow$get("java_exe"),
  java_tmp = opts_flow$get("java_tmp"),
  mutect_jar = opts_flow$get("mutect_jar"),
  cpu_mutect = opts_flow$get("cpu_mutect"),
  mem_mutect = opts_flow$get("java_mem"),
  ref_fasta = opts_flow$get("ref_fasta"),
  mutect_opts = opts_flow$get("mutect_opts"))

Arguments

tumor_bam	path to a tumor bam file
normal_bam	path to a normal bam file
samplename	name of the sample, to be added to the flowmat
outfile	output file name [optional]
is_merged	specify if the input bam is already split by chromosomes (FALSE) or is a merged file with all chromosome (TRUE). [FALSE]
split_by_chr	fork running mutect by chromosome to make it faster.
java_exe	path to java's executable [java]
java_tmp	path to a temp folder to be used by java
mutect_jar	path to mutect's jar file
cpu_mutect	integer specifying number of thread to be used per mutect fork
mem_mutect	amount of memory to be used by mutect [-Xmx12g]
ref_fasta	path to the reference genome in fasta format
mutect_opts	additional arguments passed onto mutect

Examples

## Not run: 

x = "tumor.bam"
y = "normal.bam"

out = mutect(x, y, is_merged = TRUE)


## End(Not run)

flow-r/ngsflows documentation built on May 16, 2019, 1:25 p.m.