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MRCIEU · Jan 16, 2025 · f3b84f0 · f3b84f0
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diff --git a/resources/genotypes/hm3_prune_th_hg19.bed.gz b/resources/genotypes/hm3_prune_th_hg19.bed.gz
diff --git a/resources/genotypes/hm3_prune_th_hg38.bed.gz b/resources/genotypes/hm3_prune_th_hg38.bed.gz
diff --git a/test/prune_list/remove_ld.r b/test/prune_list/remove_ld.r
@@ -0,0 +1,15 @@
+library(data.table)
+library(dplyr)
+
+hg19 <- fread("resources/genotypes/hm3_prune_th_hg19.bed.gz") %>% as_tibble()
+hg38 <- fread("resources/genotypes/hm3_prune_th_hg38.bed.gz") %>% as_tibble()
+
+a <- subset(hg19, (V1 == 5 & V2 >= 44000000 & V3 <= 51500000) | (V1 == 6 & V2 >= 25000000 & V3 <= 33500000) | (V1 == 8 & V2 >= 8000000 & V3 <= 12000000) | (V1 == 11 & V2 >= 45000000 & V3 <= 57000000))
+
+rsids <- a$V4
+hg19 <- subset(hg19, !(V4 %in% rsids))
+hg38 <- subset(hg38, !(V4 %in% rsids))
+
+fwrite(hg19, "resources/genotypes/hm3_prune_th_hg19.bed.gz")
+fwrite(hg38, "resources/genotypes/hm3_prune_th_hg38.bed.gz")
+