BIGr (version 0.6.2)

filterVCF: Filter a VCF file

Description

This function will filter a VCF file or vcfR object and export the updated version

Usage

filterVCF(
  vcf.file,
  filter.OD = NULL,
  filter.BIAS.min = NULL,
  filter.BIAS.max = NULL,
  filter.DP = NULL,
  filter.MPP = NULL,
  filter.PMC = NULL,
  filter.MAF = NULL,
  filter.SAMPLE.miss = NULL,
  filter.SNP.miss = NULL,
  ploidy,
  output.file = NULL
)

Value

A gzipped vcf file

Arguments

vcf.file

vcfR object or path to VCF file. Can be unzipped (.vcf) or gzipped (.vcf.gz).

filter.OD

Updog filter

filter.BIAS.min

Updog filter (requires a value for both BIAS.min and BIAS.max)

filter.BIAS.max

Updog filter (requires a value for both BIAS.min and BIAS.max)

filter.DP

Total read depth at each SNP filter

filter.MPP

Updog filter

filter.PMC

Updog filter

filter.MAF

Minor allele frequency filter

filter.SAMPLE.miss

Sample missing data filter

filter.SNP.miss

SNP missing data filter

ploidy

The ploidy of the species being analyzed

output.file

output file name (optional). If no output.file name provided, then a vcfR object will be returned.

Details

This function will input a VCF file or vcfR object and filter based on the user defined options. The output file will be saved to the location and with the name that is specified. The VCF format is v4.3

Examples

## Use file paths for each file on the local system

#Temp location (only for example)
output_file <- tempfile()

filterVCF(vcf.file = system.file("iris_DArT_VCF.vcf.gz", package = "BIGr"),
           filter.OD = 0.5,
           filter.MAF = 0.05,
           ploidy = 2,
           output.file = output_file)

# Removing the output for the example
rm(output_file)

##The function will output the filtered VCF to the current working directory