vcfWrite: Utility to write VCF file

In smgogarten/GWASTools: Tools for Genome Wide Association Studies

Utility to write VCF file

Description

genoDataAsVCF creates a VCF-class object.

vcfWrite writes a VCF file from a GenotypeData object.

vcfCheck compares the genotypes in a VCF file to the corresponding genotypes in genoData.

Usage

genoDataAsVCF(genoData, sample.col="scanID",
              id.col="snpID", qual.col=NULL, filter.cols=NULL,
              info.cols=NULL, scan.exclude=NULL, snp.exclude=NULL,
              scan.order=NULL, ref.allele=NULL)

vcfWrite(genoData, vcf.file="out.vcf", sample.col="scanID",
         id.col="snpID", qual.col=NULL, filter.cols=NULL,
         info.cols=NULL, scan.exclude=NULL, snp.exclude=NULL,
         scan.order=NULL, ref.allele=NULL, block.size=1000, verbose=TRUE)

vcfCheck(genoData, vcf.file,
         sample.col="scanID", id.col="snpID",
         scan.exclude=NULL, snp.exclude=NULL,
         block.size=1000, verbose=TRUE)

Arguments

genoData	A GenotypeData object with scan and SNP annotation.
vcf.file	Filename for the output VCF file.
sample.col	name of the column in the scan annotation to use as sample IDs in the VCF file
id.col	name of the column in the SNP annotation to use as "ID" column in the VCF file
qual.col	name of the column in the SNP annotation to use as "QUAL" column in the VCF file
filter.cols	vector of column names in the SNP annotation to use as "FILTER" column in the VCF file. These columns should be logical vectors, with TRUE for SNPs to be filtered. Any SNPs with a value of FALSE for all filter columns will be set to "PASS".
info.cols	vector of column names in the SNP annotation to concatenate for the "INFO" column in the VCF file.
scan.exclude	vector of scanIDs to exclude from creation or checking of VCF file
snp.exclude	vector of snpIDs to exclude from creation or checking of VCF file
scan.order	vector of scanIDs to include in VCF file, in the order in which they should be written
ref.allele	vector of "A" or "B" values indicating where allele A or allele B should be the reference allele for each SNP. Default is to use allele A as the reference allele.
block.size	Number of SNPs to read from genoData at a time
verbose	logical for whether to show progress information.

Details

REF will be alleleA and ALT will be alleleB.

vcfCheck compares the genotypes (diploid only) in a VCF file to the corresponding genotypes in genoData. It stops with an error when it detects a discordant genotype. It assumes that the "ID" column of the VCF file has unique values that can be matched with a column in the SNP annotation. The VCF file may contain additional samples or SNPs not present in the genoData; these records will be automaticlaly excluded from the check. Users may exclude additional SNPs and samples (i.e. those overlapping with genoData) using the scan.exclude and snp.exclude arguments.

Author(s)

Stephanie Gogarten, Michael Lawrence, Sarah Nelson

References

The variant call format and VCFtools. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R; 1000 Genomes Project Analysis Group. Bioinformatics. 2011 Aug 1;27(15):2156-8. Epub 2011 Jun 7.

See Also

snpgdsVCF2GDS

Examples

library(GWASdata)
library(VariantAnnotation)
gdsfile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
data(illuminaSnpADF, illuminaScanADF)
genoData <- GenotypeData(GdsGenotypeReader(gdsfile),
  scanAnnot=illuminaScanADF, snpAnnot=illuminaSnpADF)
vcf <- genoDataAsVCF(genoData, id.col="rsID")
vcf

vcffile <- tempfile()
vcfWrite(genoData, vcffile, id.col="rsID", info.cols="IntensityOnly")
vcf <- readVcf(vcffile, "hg18")
vcf
vcfCheck(genoData, vcffile, id.col="rsID")
close(genoData)
unlink(vcffile)

smgogarten/GWASTools documentation built on Nov. 10, 2024, 9:54 p.m.