vcftobd {BinaryDosage}

Convert a VCF file to a binary dosage file

Description

Routine to read information from a VCF file and create a binary dosage file. The function is designed to use files return from the Michigan Imputation Server but will run on other VCF files if they contain dosage and genetic probabilities. Note: This routine can take a long time to run if the VCF file is large.

Usage

vcftobd(
  vcffiles,
  gz = FALSE,
  bdfiles,
  format = 4L,
  subformat = 0L,
  snpidformat = 0,
  bdoptions = character(0)
)

Arguments

vcffiles

A vector of file names. The first is the name of the vcf file. The second is name of the file that contains information about the imputation of the SNPs. This file is produced by minimac 3 and 4.

gz

Indicator if VCF file is compressed using gzip. Default value is FALSE.

bdfiles

Vector of names of the output files. The binary dosage file name is first. The family and map files follow. For format 4, no family and map file names are needed.

format

The format of the output binary dosage file. Allowed values are 1, 2, 3, and 4. The default value is 4. Using the default value is recommended.

subformat

The subformat of the format of the output binary dosage file. A value of 1 or 3 indicates that only the dosage value is saved. A value of 2 or 4 indicates the dosage and genetic probabilities will be output. Values of 3 or 4 are only allowed with formats 3 and 4. If a value of zero if provided, and genetic probabilities are in the vcf file, subformat 2 will be used for formats 1 and 2, and subformat 4 will be used for formats 3 and 4. If the vcf file does not contain genetic probabilities, subformat 1 will be used for formats 1 and 2, and subformat 3 will be used for formats 3 and 4. The default value is 0.

snpidformat

The format that the SNP ID will be saved as. -1 SNP ID not written 0 - same as in the VCF file 1 - chromosome:location 2 - chromosome:location:reference_allele:alternate_allele If snpidformat is 1 and the VCF file uses format 2, an error is generated. Default value is 0.

bdoptions

Character array containing any of the following value, "aaf", "maf", "rsq". The presence of any of these values indicates that the specified values should be calculates and stored in the binary dosage file. These values only apply to format 4.

Value

None

Examples

# Find the vcf file names
vcf1afile <- system.file("extdata", "set1a.vcf", package = "BinaryDosage")
vcf1ainfo <- system.file("extdata", "set1a.info", package = "BinaryDosage")
bdfiles <- tempfile()
# Convert the file
vcftobd(vcffiles = c(vcf1afile, vcf1ainfo), bdfiles = bdfiles)
# Verify the file was written correctly
bdinfo <- getbdinfo(bdfiles)