museCalling: museCalling

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

Description

Tumor-normal pair somatic variant calling using MuSE

Usage

museCalling(
  tumor_file,
  normal_file,
  sample_name,
  ref,
  out_path,
  muse,
  af_only_gnomad,
  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.
muse	Path of MuSE binary.
af_only_gnomad	Genome aggregation database used as a germline resource. Have to be base on the same reference genome as 'ref'. gnomAD

Examples

## Not run: 
museCalling(tumor_file = 'raw/sample_tumor.bam',
            normal_file = 'raw/sample_normal.bam',
            sample_name = 'sample'
            ref = 'ref/hg38.fa',
            out_path = 'rst',
            muse = '/bin/MuSE',
            af_only_gnomad = 'hg38/af-only-gnomad.hg38.vcf.gz')

## End(Not run)

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