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Add LinSight_Score to cre repo #51

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3 changes: 2 additions & 1 deletion cre.gemini2txt.vcf2db.sh
Original file line number Diff line number Diff line change
Expand Up @@ -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,
LinSight_Score"
else
noncoding_anno="00 as noncoding"
fi
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2 changes: 1 addition & 1 deletion cre.vcf2db.R
Original file line number Diff line number Diff line change
Expand Up @@ -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", "LinSight_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)
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