snpgdsVCF2GDS {SNPRelate} | R Documentation

## 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)

[Package SNPRelate version 1.26.0 Index]