added tcag filter

naumenko-sa · Jul 10, 2019 · 6683306 · 6683306
1 parent a48054f
commit 6683306
Showing 1 changed file with 11 additions and 0 deletions.
diff --git a/cre.panel_filter.tcag.R b/cre.panel_filter.tcag.R
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+###############################################################################
+# Filter TCAG small variant report
+###############################################################################
+library(tidyverse)
+
+args = commandArgs(trailingOnly = T)
+input_table <- read_tsv(args[1])
+panel <- read_csv(args[2])
+filtered_table <- input_table %>% filter(FILTER=="PASS", gene_symbol %in% panel$Gene_name,
+                                         !typeseq_priority %in% c("intronic"))
+write_excel_csv(filtered_table, args[3])