realignBamBwa: realignBamBwa
In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

This function realigns bam files using a defined reference genome and bwa being possible to use paired or single end data (type will be detected automatically)

1	realignBamBwa(inputFile, ref, outPath, threads, removeOpt)

`inputFile`	Path of the fastq file to align.
`ref`	Path where the reference genome is save.
`outPath`	Path where the output of the analysis will be saved.
`threads`	Number of threads to use in the analysis.
`removeOpt`	Remove old bam option (yes or no)

## Not run: 
inputFile <- 'raw/sample.bam'
ref <- 'ref/hg38.fa'
outPath <- 'rst'
threads <- 2
removeOpt <- 'yes'

realignBamBwa(inputFile, ref, outPath, threads, removeOpt)

## End(Not run)