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

Aligned and co-cleaned BAM files are processed as tumor-normal pairs. Variant calling is performed using six separate pipelines:

variantCalling(
  tumor_file,
  normal_file,
  sample_name,
  ref = "/imppc/labs/lplab/share/marc/refgen/hg38/hg38.fa",
  out_path,
  threads = 1,
  gatk4 = "/imppc/labs/lplab/share/bin/gatk-4.1.3.0/gatk",
  muse = "/imppc/labs/lplab/share/marc/repos/MuSE/MuSE",
  bwa = "bwa",
  samblaster = "samblaster",
  sambamba = "sambamba",
  samtools = "samtools",
 
    somatic_sniper = "/imppc/labs/lplab/share/marc/repos/somatic-sniper/build/bin/bam-somaticsniper",
  varscan2 = "/imppc/labs/lplab/share/marc/repos/varscan/VarScan.v2.4.4.jar",
  manta = "/software/debian-8/bio/manta-1.4.0",
  strelka2 = "/soft/bio/strelka-2.9.3",
 
    af_only_gnomad = "/imppc/labs/lplab/share/marc/refgen/hg38/af-only-gnomad.hg38.vcf.gz",
  pindel = "/soft/bio/pindel/pindel",
  centromeres_telomeres = "/imppc/labs/lplab/share/marc/refgen/hg38/centromeres.bed",
  perl = "perl",
  python_radia = "/imppc/labs/lplab/share/marc/repos/miniconda/bin/python2.7",
  radia_path = "/imppc/labs/lplab/share/marc/repos/radia/scripts",
  bcftools = "bcftools",
  tumor_vcf_id = "TUMOR",
  fpfilter = "/imppc/labs/lplab/share/marc/repos/fpfilter-tool/fpfilter.pl",
  bam_readcount = "bam-readcount"
)

`tumor_file`	Tumor bam to file to perform the variant calling.
`normal_file`	Normal bam to file to perform the variant calling.
`ref`	Path for the reference genome to use for the alignment (fasta format) and the corresponding indexes generated with bwa index and a dictionary index file generated by CreateSequenceDictionary gatk tool.
`out_path`	Path where the output of the analysis will be saved.
`threads`	Number of threads to use in the analysis.
`gatk4`	Path of GATK4 binary.
`muse`	Path of MuSE binary.
`bwa`	Path of bwa binary.
`samblaster`	Path of samblaster binary.
`sambamba`	Path of sambamba binary
`samtools`	Path of samtools binary.
`somatic_sniper`	Path of SomaticSniper binary.
`manta`	Path of manta binary.
`strelka2`	Path of strelka2 binary.
`af_only_gnomad`	Genome aggregation database used as a germline resource. Have to be base on the same reference genome as 'ref'. gnomAD
`pindel`	Path of Pindel binary.
`centromeres_telomeres`	Bed file with the centromers and/or telomeres base on the same reference genome as 'ref'.
`perl`	Path of perl executable.
`python_radia`	Path to the python binary with all the RADIA prerequisites.
`tumor_vcf_id`	Id of the tumor sample in vcf. By default 'TUMOR'.

## Not run: 
variantCalling(tumor_file = 'NET-10_TI_mkdup_sub_0005.bam',
               normal_file = 'NET-10_BL_mkdup_sub_0005.bam',
               sample_name = 'NET-10',
               ref = 'hg38.fa',
               out_path = 'processed/vcf',
               threads = 2)

## End(Not run)