On branch master

bin/varscanSomaticFilter.py added

bin/varscanSomaticFilter.py

@@ -0,0 +1,27 @@
+#!/usr/bin/env python
+
+import sys
+
+def main():
+    infile = open(sys.argv[1])
+    outfile = open(sys.argv[2], 'w')
+    depth_thred = int(sys.argv[3])
+
+    for line in infile:
+        if line[0:5] == 'chrom':
+            continue
+
+        fields = line.split('\t')
+        a_T = int(fields[8])
+        b_T = int(fields[9])
+        d_T = a_T + b_T
+        somatic_status = fields[12]
+
+        if d_T >= depth_thred and somatic_status == 'Somatic':
+            outfile.write(line)
+
+    infile.close()
+    outfile.close()
+
+if __name__ == '__main__':
+    main()