added zygosity columns to the clinical report

naumenko-sa · Feb 1, 2019 · 072de57 · 072de57
1 parent d9b0601
commit 072de57
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/cre.topmed.R b/cre.topmed.R
@@ -20,7 +20,7 @@ get_af_by_rsid <- function(rs_id){
     # from Johar 2016
     # rs_id <- "rs202193903"
     # rs_id = "rs903331232"
-    rs_id = "rs1129038"
+    # rs_id = "rs1129038"
     #- not found
     #ls("package:MafDb.TOPMed.freeze5.hg19")
     mafdb <- MafDb.TOPMed.freeze5.hg19

diff --git a/cre.vcf2db.R b/cre.vcf2db.R
@@ -671,7 +671,8 @@ clinical_report <- function(project,samples){
 
     filtered_report <- subset(full_report, 
                Quality > 1000 & Gnomad_af_popmax < 0.005 & Frequency_in_C4R < 6 & max_alt >=20,
-               select = c("Position", "GNOMAD_Link", "Ref", "Alt", "Gene", paste0("Burden.",samples),
+               select = c("Position", "GNOMAD_Link", "Ref", "Alt", "Gene", paste0("Zygosity.", samples), 
+                          paste0("Burden.",samples),
                         "Variation", "Info", "Refseq_change", "Omim_gene_description", "Omim_inheritance",
                         "Orphanet", "Clinvar", "Frequency_in_C4R",
                         "Gnomad_af_popmax", "Gnomad_af", "Gnomad_ac", "Gnomad_hom",