postCalling: postCalling

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

Description

Vcf sorting, normalization and reheader of the vcf generated unsing 'variantCalling' for posterior annotation. Input file have to present the *_PASS.vcf format and being uncompressed.

Usage

postCalling(
  pass_vcf,
  gatk4 = "/imppc/labs/lplab/share/bin/gatk-4.1.3.0/gatk",
  ref,
  bcftools = "bcftools",
  out_path
)

Arguments

pass_vcf	Vcf to apply post-calling processing. It should be descompressed and *_PASS.vcf format.
gatk4	Path of GATK4 binary.
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.

Examples

## Not run: 
postCalling(pass_vcf = 'raw/sample_tumor.bam',
            gatk4 = 'bin/gatk-4.1.3.0/gatk',
            ref = 'ref/hg38.fa',
            bcftools = 'bcftools')

## End(Not run)

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