varscan2Calling: varscan2Calling

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

Description

Tumor-normal pair somatic variant calling using VarScan2.

Usage

varscan2Calling(
  tumor_file,
  normal_file,
  sample_name,
  ref,
  out_path,
  varscan2,
  samtools,
  fpfilter,
  perl,
  bcftools
)

Arguments

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.
samtools	Path of samtools binary.
perl	Path of perl executable.

Examples

## Not run: 
varscan2Calling(tumor_file = 'raw/sample_tumor.bam',
               normal_file = 'raw/sample_normal.bam',
               sample_name = 'sample'
               ref = 'ref/hg38.fa',
               out_path = 'rst',
               varscan2 = '/bin/VarScan.v2.4.4.jar',
               threads = 2,
               samtools = '/bin/samtools')

## End(Not run)

msubirana/ergWgsTools documentation built on June 8, 2020, 8:07 a.m.