including position in variant file

MRCIEU · Oct 20, 2024 · b54e315 · b54e315
1 parent 660981b
commit b54e315
Showing 1 changed file with 2 additions and 0 deletions.
diff --git a/resources/genotypes/generate_variant_reference.r b/resources/genotypes/generate_variant_reference.r
@@ -21,6 +21,8 @@ l <- lapply(afreqlist, \(fn) {
     a$EA[a$flipped] <- a$OA[a$flipped]
     a$OA[a$flipped] <- temp
     a$CHR <- as.character(a$CHR)
+    a$POS <- as.numeric(sub(".*:(.*)_(.*)_(.*)", "\\1", a$SNP))    
+    a <- dplyr::select(a, CHR, POS, SNP, OA, EA, EAF, OBS_CT, flipped, POS)
     str(a)
     a
 }) %>% bind_rows()