fpfilterTool: fpfilterTool

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

Description

False postive filter parser for label low quality reads

Usage

fpfilterTool(
  vcf,
  tumor_file,
  sample_name,
  ref,
  fpfilter,
  perl,
  out_path,
  bam_readcount,
  tumor_vcf_id = "TUMOR"
)

Arguments

tumor_file	Tumor 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.
perl	Path of perl executable.
out_path	Path where the output of the analysis will be saved.
tumor_vcf_id	Id of the tumor sample in vcf. By default 'TUMOR'.

Examples

## Not run: 
fpfilterTool(vcf = 'vcf/sample.vcf',
             tumor_file = 'raw/sample_tumor.bam',
               sample_name = 'sample'
               ref = 'ref/hg38.fa',
               out_path = 'rst',
               perl = 'perl',
               fpfilter = 'fpfilter-tool/fpfilter.pl',
               bam_readcount = 'bam_readcount')

## End(Not run)

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