pindelCalling: pindelCalling

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

Description

Tumor-normal pair somatic variant calling using Pindel

Usage

pindelCalling(
  tumor_file,
  normal_file,
  sample_name,
  ref,
  out_path,
  pindel,
  sambamba,
  samtools,
  threads,
  perl,
  gatk4,
  centromeres_telomeres,
  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.
pindel	Path of Pindel binary.
sambamba	Path of sambamba binary
samtools	Path of samtools binary.
threads	Number of threads to use in the analysis.
perl	Path of perl executable.
gatk4	Path of GATK4 binary.
centromeres_telomeres	Bed file with the centromers and/or telomeres base on the same reference genome as 'ref'.

Examples

## Not run: 
pindelCalling(tumor_file = 'raw/sample_tumor.bam',
               normal_file = 'raw/sample_normal.bam',
               sample_name = 'sample'
               ref = 'ref/hg38.fa',
               out_path = 'rst')

## End(Not run)

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