Mercurial > repos > saskia-hiltemann > virtual_normal_analysis

diff vcf2lv.sh @ 2:885ba15c2564 draft

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Uploaded
author saskia-hiltemann
date Mon, 03 Aug 2015 05:45:16 -0400
parents 1209f18a5a83
children 58815aed4ec3
line wrap: on
line diff
--- a/vcf2lv.sh	Mon Aug 03 05:03:16 2015 -0400
+++ b/vcf2lv.sh	Mon Aug 03 05:45:16 2015 -0400
@@ -19,7 +19,7 @@
 		count=0;
 		
 		#output new header
-		print "variantId", "chromosome", "begin", "end", "varType", "reference", "alleleSeq", "xRef"
+		print "variantId", "chromosome", "begin", "end", "varType", "reference", "alleleSeq"
 	}{
 
 		if(substr($0,1,1)!="#" && $5 != "."){ #skip header or nonvariant entries (period in ALT column)
@@ -85,8 +85,7 @@
 		
 				#print output variant(s)
 		
-				if(chromosome != "chrM")
-					print count, chromosome, start, end, varType, reference, alleleSeq, ""
+				print count, chromosome, start, end, varType, reference, alleleSeq
 			
 				count+=1
 			}