The cutoff file contains the number of DeNovoGear calls for a particular posterior probability cutoff. Extract the same number of SamTools calls. If there is a tie in the last Likelihood Ratio value then pick all calls with that CLR value

extractCalls.sh

#Avinash Ramu, WUSTL
#! /bin/bash

#The cutoff file contains the number of DeNovoGear calls for a particular posterior probability cutoff. Extract the same number of SamTools calls. If there is a tie in the last Likelihood Ratio value then pick all calls with that CLR value 

cutoff_f=1e-8Cutoffs
STop=STop_nonX_sorted

for cutoff in `cat $cutoff_f`
do 
 echo $cutoff
 awk -v cutoff=$cutoff 'BEGIN { count=0; pc=0;} {count++; if(count<=cutoff || pc==$3) {print; pc=$3}}' $STop > ${STop}_$cutoff
done

is there a quick parser for filtering Denovogear outputs?