From 0d22325b9aabe7345b629b271c36dae49bdf9903 Mon Sep 17 00:00:00 2001 From: Ilham Abbasi Date: Thu, 18 Apr 2024 13:44:47 -0400 Subject: [PATCH 1/2] add ncER score to non-coding annotations --- cre.gemini2txt.vcf2db.sh | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/cre.gemini2txt.vcf2db.sh b/cre.gemini2txt.vcf2db.sh index 19e2fcf..500d4cb 100755 --- a/cre.gemini2txt.vcf2db.sh +++ b/cre.gemini2txt.vcf2db.sh @@ -50,7 +50,8 @@ then enh_cellline_tissue as ENH_cellline_tissue, tf_binding_sites as TF_binding_sites, c4r_wgs_counts as C4R_WGS_counts, - c4r_wgs_samples as C4R_WGS_samples" + c4r_wgs_samples as C4R_WGS_samples, + ncER_score" else noncoding_anno="00 as noncoding" fi From 07b402c4900fe96eeb553736b195062f42714285 Mon Sep 17 00:00:00 2001 From: Ilham Abbasi Date: Thu, 18 Apr 2024 13:48:50 -0400 Subject: [PATCH 2/2] add ncER score annotations for non-coding variants --- cre.vcf2db.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/cre.vcf2db.R b/cre.vcf2db.R index ab5c658..e86ce32 100644 --- a/cre.vcf2db.R +++ b/cre.vcf2db.R @@ -429,7 +429,7 @@ select_and_write2 <- function(variants, samples, prefix, type) { print(colnames(variants)) if (type == 'wgs' || type == 'denovo'){ - noncoding_cols <- c("DNaseI_hypersensitive_site", "CTCF_binding_site", "ENH_cellline_tissue", "TF_binding_sites") + noncoding_cols <- c("DNaseI_hypersensitive_site", "CTCF_binding_site", "ENH_cellline_tissue", "TF_binding_sites", "ncER_score") wgs_counts <- c("C4R_WGS_counts", "C4R_WGS_samples") variants$C4R_WGS_counts[variants$C4R_WGS_counts == "None"] <- 0 variants$C4R_WGS_counts <- as.integer(variants$C4R_WGS_counts)