strelka: strelka2
In msubirana/ergWgsTools: What the Package Does (One Line, Title Case)

Description Usage Arguments Format Examples

Snvs and indels calling of paired tumor-normal wgs using manta

strelka

`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
`indelCandidates`	For the somatic workflow, the best-practice recommendation is to run the Manta SV and indel caller on the same set of samples first, then supply Manta's candidate indels as input to Strelka

An object of class character of length 1.

## 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'
indelCandidates <- /results/variants/candidateSmallIndels.vcf.gz
strelka2(normal = normal,
      tumor = tumor,
      ref = ref,
      outPath = outPath,
      cores = cores,
      outName = outName)


## End(Not run)