Update extraction_1KG.R

R/extraction_1KG.R

@@ -129,6 +129,9 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
     vcf <- utils::read.delim(
         text = gsub("##", "!", txt), header = TRUE, comment.char = "!", stringsAsFactors = FALSE)
     
+    # Discard multi-allelic markers.
+    vcf <- vcf[grep(",", vcf$ALT, invert = TRUE), ]
+    
     # Throw error if SNP not found
     if (nrow(vcf) < 1) {
         msg <- paste("SNP ", chrom, ":", start, "-", end, " not found", sep = "")
@@ -140,10 +143,7 @@ get_vcf <- function(chrom, start, end, pop = NA, path = "", web = TRUE) {
     # Assign the standard column names and sample identifiers.
     colnames(vcf)[1] <- "CHROM"
     
-    # Discard multi-allelic markers.
-    vcf <- vcf[grep(",", vcf$ALT, invert = TRUE), ]
-    
-    # Select the genotype columns that belong to a particular population.
+        # Select the genotype columns that belong to a particular population.
     if (pop %in% pops) {
         vcf <- vcf[,c(rep(TRUE, 9), pops == pop)]
     } else if (pop %in% superpops) {