snpgdsVCF2GDS: Reformat VCF file(s)

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

Reformat VCF file(s)

Description

Reformat Variant Call Format (VCF) file(s)

Usage

snpgdsVCF2GDS(vcf.fn, out.fn, method=c("biallelic.only", "copy.num.of.ref"),
    snpfirstdim=FALSE, compress.annotation="LZMA_RA", compress.geno="",
    ref.allele=NULL, ignore.chr.prefix="chr", verbose=TRUE)

Arguments

vcf.fn	the file name of VCF format, vcf.fn can be a vector, see details
out.fn	the file name of output GDS
method	either "biallelic.only" by default or "copy.num.of.ref", see details
snpfirstdim	if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc)
compress.annotation	the compression method for the GDS variables, except "genotype"; optional values are defined in the function add.gdsn
compress.geno	the compression method for "genotype"; optional values are defined in the function add.gdsn
ref.allele	NULL or a character vector indicating reference allele (like "A", "G", "T", NA, ...) for each site where NA to use the original reference allele in the VCF file(s). The length of character vector should be the total number of variants in the VCF file(s).
ignore.chr.prefix	a vector of character, indicating the prefix of chromosome which should be ignored, like "chr"; it is not case-sensitive
verbose	if TRUE, show information

Details

GDS – Genomic Data Structures used for storing genetic array-oriented data, and the file format used in the gdsfmt package.

VCF – The Variant Call Format (VCF), which is a generic format for storing DNA polymorphism data such as SNPs, insertions, deletions and structural variants, together with rich annotations.

If there are more than one file names in vcf.fn, snpgdsVCF2GDS will merge all dataset together if they all contain the same samples. It is useful to combine genetic/genomic data together if VCF data are divided by chromosomes.

method = "biallelic.only": to exact bi-allelic and polymorhpic SNP data (excluding monomorphic variants); method = "copy.num.of.ref": to extract and store dosage (0, 1, 2) of the reference allele for all variant sites, including bi-allelic SNPs, multi-allelic SNPs, indels and structural variants.

Haploid and triploid calls are allowed in the transfer, the variable snp.id stores the original the row index of variants, and the variable snp.rs.id stores the rs id.

When snp.chromosome in the GDS file is character, SNPRelate treats a chromosome as autosome only if it can be converted to a numeric value ( like "1", "22"). It uses "X" and "Y" for non-autosomes instead of numeric codes. However, some software format chromosomes in VCF files with a prefix "chr". Users should remove that prefix when importing VCF files by setting ignore.chr.prefix = "chr".

The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variation (SNV), insertion/deletion polymorphism (indel) and structural variation calls. It is strongly suggested to use SeqArray for large-scale whole-exome and whole-genome sequencing variant data instead of SNPRelate.

Value

Return the file name of GDS format with an absolute path.

Author(s)

Xiuwen Zheng

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.

http://corearray.sourceforge.net/

See Also

snpgdsBED2GDS

Examples

# the VCF file
vcf.fn <- system.file("extdata", "sequence.vcf", package="SNPRelate")
cat(readLines(vcf.fn), sep="\n")

snpgdsVCF2GDS(vcf.fn, "test1.gds", method="biallelic.only")
snpgdsSummary("test1.gds")

snpgdsVCF2GDS(vcf.fn, "test2.gds", method="biallelic.only", snpfirstdim=TRUE)
snpgdsSummary("test2.gds")

snpgdsVCF2GDS(vcf.fn, "test3.gds", method="copy.num.of.ref", snpfirstdim=TRUE)
snpgdsSummary("test3.gds")

snpgdsVCF2GDS(vcf.fn, "test4.gds", method="copy.num.of.ref")
snpgdsSummary("test4.gds")

snpgdsVCF2GDS(vcf.fn, "test5.gds", method="copy.num.of.ref",
    ref.allele=c("A", "T", "T", "T", "A"))
snpgdsSummary("test5.gds")



# open "test1.gds"
(genofile <- snpgdsOpen("test1.gds"))

read.gdsn(index.gdsn(genofile, "sample.id"))
read.gdsn(index.gdsn(genofile, "snp.rs.id"))
read.gdsn(index.gdsn(genofile, "genotype"))

# close the file
snpgdsClose(genofile)


# open "test2.gds"
(genofile <- snpgdsOpen("test2.gds"))

read.gdsn(index.gdsn(genofile, "sample.id"))
read.gdsn(index.gdsn(genofile, "snp.rs.id"))
read.gdsn(index.gdsn(genofile, "genotype"))

# close the file
snpgdsClose(genofile)


# open "test3.gds"
(genofile <- snpgdsOpen("test3.gds"))

read.gdsn(index.gdsn(genofile, "sample.id"))
read.gdsn(index.gdsn(genofile, "snp.rs.id"))
read.gdsn(index.gdsn(genofile, "genotype"))

# close the file
snpgdsClose(genofile)


# open "test4.gds"
(genofile <- snpgdsOpen("test4.gds"))

read.gdsn(index.gdsn(genofile, "sample.id"))
read.gdsn(index.gdsn(genofile, "snp.rs.id"))
read.gdsn(index.gdsn(genofile, "snp.allele"))
read.gdsn(index.gdsn(genofile, "genotype"))

# close the file
snpgdsClose(genofile)


# open "test5.gds"
(genofile <- snpgdsOpen("test5.gds"))

read.gdsn(index.gdsn(genofile, "sample.id"))
read.gdsn(index.gdsn(genofile, "snp.rs.id"))
read.gdsn(index.gdsn(genofile, "snp.allele"))
read.gdsn(index.gdsn(genofile, "genotype"))

# close the file
snpgdsClose(genofile)


# delete the temporary files
unlink(paste("test", 1:5, ".gds", sep=""), force=TRUE)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.