BEGIN{ FS=","; #in: paralyzer format # 1 2 3 4 5 6 7 8 9 10 11 12 #Chromosome,Strand,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ModeScore,ConversionLocationCount,ConversionEventCount,NonConversionEventCount #out: bed format # 1 2 3 4 _ 5 _ 6 _ 7 _ 8 _ 9 _ 10 11 12 #Chromosome,ClusterStart,ClusterEnd,ClusterID,ClusterSequence,ReadCount,ModeLocation,ConversionLocationCount,ConversionEventCount,NonConversionEventCount,ModeScore,Strand }{ if (substr($1,1,4)!="Chro") { if (($2=="+")&&($11>5)) print $1"\t"$3-1"\t"$4-1"\t"$5"_"$6"_"$7"_"$8"_"$10"_"$11"_"$12"\t"$9"\t"$2; } }