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tasks/MIEpos2bed.wdl

@@ -8,9 +8,9 @@ task MIEpos2bed {
 	
 	command <<<
 
-		cat ${mie_file} | awk '{print $1,$2,$2}' > ${sample_name}.${chromo}.allvariants.bed	
+		cat ${mie_file} | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.allvariants.bed	
 
-		cat ${mie_file} | grep -v '1:1:1' | awk '{print $1,$2,$2}' > ${sample_name}.${chromo}.mie.bed			
+		cat ${mie_file} | grep -v '1:1:1' | awk '{print $1"\t"$2"\t"$2}' > ${sample_name}.${chromo}.mie.bed			
 
 	>>>