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

SVs calling of paired tumor-normal wgs using manta

1	manta(normal, tumor, ref, outPath, cores, outName)

`normal`	Normal bam file.
`tumor`	Tumour bam file.
`ref`	Reference genome.
`outPath`	Path where the output of the analysis will be saved.
`cores`	Number of cores to use.
`outName`	Name for the output file for the paired tumor normal analysis

## Not run: 

normal <- 'raw/sample1_BL.bam'
tumor <- 'raw/sample1_TI.bam'
ref <- '/imppc/labs/lplab/share/marc/refgen/hg38/hg38.fa'
outPath <- 'dir/vcf'
cores <- 4
outName <- 'sample1'
manta(normal = normal,
      tumor = tumor,
      ref = ref,
      outPath = outPath,
      cores = cores,
      outName = outName)


## End(Not run)