bwa: bwa

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

Description

A wrapper function to run BWA.

Usage

bwa(bwa.method, fq1, fq2, output.dir, sample.name, ref.fa, bwa.idx, bwa_thread_number=4, run.cmd=TRUE, mc.cores=1)

Arguments

bwa.method	bwa algorithms of mem and aln can be used(mem: for paired-end data, aln: for single-end data)
fq1	Path to read1 fastq files
fq2	Path to read2 fastq files (bwa-mem only)
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Path to reference fasta file
bwa.idx	Path to bwa index files
bwa.thread.number	A parameter value for -t in BWA. A numeric value of the number of threads (default: 4)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome. "bwa" can be run with option either of BWA-mem or BWA-aln.

Value

Aligned BAM files

References

Fast and accurate short read alignment with Burrows-Wheeler transform

See Also

http://bio-bwa.sourceforge.net/bwa.html

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