no info

tasks/MIEpos2bed.wdl

@@ -10,9 +10,9 @@ task MIEpos2bed {
 
 		python /opt/vcf2bed.py ${mie_file} ${sample_name}.${chromo}.info.txt
 
-		cat ${mie_file} | awk '{ if ($3 == 0) { print } }' | cut -f1,8,9 > ${sample_name}.${chromo}.allvariants.bed	
+		cat ${sample_name}.${chromo}.info.txt | grep -v '0:4:4' | grep -v '1:4:4' | awk '{ if ($3 != 0) { print } }' | cut -f1,8,9 > ${sample_name}.${chromo}.allvariants.bed	
 
-		cat ${mie_file} | awk '{ if ($3 == 0) { print } }' | grep 'MIE' | cut -f1,8,9 > ${sample_name}.${chromo}.mie.bed			
+		cat ${sample_name}.${chromo}.info.txt | grep -v '0:4:4' | grep -v '1:4:4' | awk '{ if ($3 != 0) { print } }' | grep 'MIE' | cut -f1,8,9 > ${sample_name}.${chromo}.mie.bed			
 
 	>>>