ezFilterVcf: Filters a VCF file and writes it back

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

Filters a VCF file and writes it back

Description

Filters a VCF file and writes it back to the specified connection.

Usage

ezFilterVcf(
  vcfFile,
  vcfFiltFile,
  discardMultiAllelic = TRUE,
  bamDataset = bamDataset,
  param = NULL
)

ezWriteVcf(vcf, vcfFiltFile)

Arguments

vcfFile	a character representing the file path of the input VCF file
vcfFiltFile	a character representing the file path of the output VCF file.
discardMultiAllelic	a logical. Removes multi allelic variants if set to TRUE.
bamDataset	a data.frame to help renaming and reordering the fields in genotype.
param	a list of parameters to extract the value from vcfFilt.minAltCount.
vcf	an object of the class VCF.

Value

Returns a filtered VCF file.

Functions

• ezWriteVcf: Writes a new VCF file.

Author(s)

Rehrauer, Hubert

Schmid, Peter

uzh/ezRun documentation built on Dec. 26, 2024, 9:53 a.m.