# Read Variant Calling Format Files `read.vcf` reads allelic data from VCF (variant calling format) files. `write.vcf` writes allelic data from an object of class `"loci"` into a VCF file. ```r read.vcf(file, from = 1, to = 10000, which.loci = NULL, quiet = FALSE) write.vcf(x, file, CHROM = NULL, POS = NULL, quiet = FALSE) ``` ## Arguments - `file`: a file name specified by either a variable of mode character, or a quoted string. - `from, to`: the loci to read; by default, the first 10,000. - `which.loci`: an alternative way to specify which loci to read is to give their indices (see `link{VCFloci}` how to obtain them). - `quiet`: a logical: should the progress of the operation be printed? - `x`: an object of class `"loci"`. - `CHROM, POS`: two vectors giving the chromosomes and (genomic) positions of the loci (typically from the output of `VCFloci`). ## Details The VCF file can be compressed (*.gz) or not. Since pegas 0.11, compressed remote files can be read (see examples). A TABIX file is not required (and will be ignored if present). In the VCF standard, missing data are represented by a dot and these are read ``as is'' by the present function without trying to substitute by `NA`. ## Note Like for `VCFloci`, the present function can read either compressed (*.gz) or uncompressed files. There should be no difference in performance between both types of files if they are relatively small (less than 1 Gb as uncompressed, equivalent to ~50 Mb when compressed). For bigger files, it is more efficient to uncompress them (if disk space is sufficient), especially if they have to be accessed several times during the same session. ## Returns an object of class `c("loci", "data.frame")`. ## Author(s) Emmanuel Paradis ## References [https://www.internationalgenome.org/wiki/Analysis/vcf4.0](https://www.internationalgenome.org/wiki/Analysis/vcf4.0) [https://github.com/samtools/hts-specs](https://github.com/samtools/hts-specs) ## See Also `VCFloci`, `read.loci`, `read.gtx`, `write.loci` ## Examples ```r ## Not run: ## Chr Y from the 1000 Genomes: a <- "https://ftp-trace.ncbi.nih.gov/1000genomes/ftp/release/20130502" b <- "ALL.chrY.phase3_integrated_v1b.20130502.genotypes.vcf.gz" ## WARNING: the name of the file above may change url <- paste(a, b, sep = "/") ## Solution 1: download first download.file(url, "chrY.vcf.gz") ## no need to uncompress: (info <- VCFloci("chrY.vcf.gz")) str(info) # show the modes of the columns ## Solution 2: read remotely (since pegas 0.11) info2 <- VCFloci(url) identical(info, info2) rm(info2) SNP <- is.snp(info) table(SNP) # how many loci are SNPs? ## compare with: table(getINFO(info, "VT")) op <- par(mfcol = c(4, 1), xpd = TRUE) lim <- c(2.65e6, 2.95e6) ## distribution of SNP and non-SNP mutations along the Y chr: plot(info$POS, !SNP, "h", col = "red", main = "non-SNP mutations", xlab = "Position", ylab = "", yaxt = "n") rect(lim[1], -0.1, lim[2], 1.1, lwd = 2, lty = 2) plot(info$POS, SNP, "h", col = "blue", main = "SNP mutations", xlab = "Position", ylab = "", yaxt = "n") rect(lim[1], -0.1, lim[2], 1.1, lwd = 2, lty = 2) par(xpd = FALSE) ## same focusing on a smaller portion of the chromosome: plot(info$POS, !SNP, "h", col = "red", xlim = lim, xlab = "Position", ylab = "", yaxt = "n") plot(info$POS, SNP, "h", col = "blue", xlim = lim, xlab = "Position", ylab = "", yaxt = "n") par(op) ## read both types of mutations separately: X.SNP <- read.vcf("chrY.vcf.gz", which.loci = which(SNP)) X.other <- read.vcf("chrY.vcf.gz", which.loci = which(!SNP)) identical(rownames(X.SNP), VCFlabels("chrY.vcf.gz")) # TRUE cat(VCFheader("chrY.vcf.gz")) ## get haplotypes for the first 10 loci: h <- haplotype(X.SNP, 1:10) ## plot their frequencies: op <- par(mar = c(3, 10, 1, 1)) plot(h, horiz=TRUE, las = 1) par(op) ## End(Not run) ```

read.vcf function