parse_vcf_output: Parse a VCF input to return a data frame with standardised...

Description Usage Arguments

View source: R/parse_vcf_output.R

Description

Parse a VCF input to return a data frame with standardised fields across callers to use for caller comparison. It only works with germline calls and for VCF from the following callers: GATK3 MuTect2, VarScan2 and VarDict.

Usage

1
parse_vcf_output(vcf_path, sample_name, caller)

Arguments

vcf_path

path to where the '.vcf' file for one sample is saved.

sample_name

character. Sample name of the current 'vcf' file.

caller

character. One of 'mutect', 'vardict' or 'varscan'.


annaquaglieri16/samplepower documentation built on Nov. 7, 2019, 11:43 p.m.