calc_allelic_freqs: Calculate allelic frequencies.

In lixiangchun/lxctk: Li Xiangchun's tool-kit (lxctk)

Description

Calculate allelic frequencies for multiple sites of multiple bam files.

Usage

calc_allelic_freqs(bamFileLists, fastaFile, OncotatorFile, outfile, lines=80, flag=FALSE, minBQ=0, minMQ=13, minDepth=8)

Arguments

bamFileLists	A vector of bam files.
fastaFile	Path to indexed reference sequence.
OncotatorFile	Oncotator annotated somatic mutation file.
outfile	Output file.
lines	Number of sites processed at a time, if there are many bam files reduced it to lower memory usage.
flag	If TRUE, a data frame will be returned.
minBQ	minBaseQuality.
minMQ	minMapQuality.
minDepth	allelic frequency is set to 0 if sequencing depth at the mutation site is < minDepth.

See Also

calc_allelic_freqs_core

Examples

library(Rsamtools)
fastaFile="/ifshk1/BC_CANCER/01bin/01bin/lixiangchun/db/hg19Virus/bwa-0.7.12/hg19Virus.fasta"
bamFileLists=read.table("/ifshk5/BC_CANCER/PROJECT/HKC11086_HUMunaX/20150716_intelligent/limiao_paper/recapseg/bam.list",header=FALSE,stringsAsFactors=FALSE)$V1
OncotatorFile="CRC_CapSeg.maf"
calc_allelic_freqs(bamFileLists, fastaFile, OncotatorFile, outfile='CRC_CapSeg_Allelic_freqs.maf', lines=20)

lixiangchun/lxctk documentation built on May 21, 2019, 6:44 a.m.