Added normalization file for 50 kb based on HGSVC trio coverage. Enable 50kb in pipeline

Snake.config.json

@@ -40,6 +40,9 @@
     "simulation_cell_count" : 100,
     "simulation_alpha" : 0.02,
 
-    "genome_size" : 3e9
+    "genome_size" : 3e9,
 
+    "normalization" : {
+        "50000_fixed" : "utils/normalization/norm.HGSVC.50kb.txt"
+    }
 }

Snakefile

@@ -26,7 +26,7 @@ rule all:
         expand("sv_calls/{sample}/{window}_fixed.{bpdens}/{method}.{chrom}.pdf",
                sample = SAMPLE,
                chrom = config["chromosomes"],
-               window = [100000],
+               window = [50000, 100000],
                bpdens = ["few","medium","more","many"],
                method = METHODS)