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You'll have to adapt it thoroughly, as the boundary conditions have changed!awk 'NR==1 {N=4}
NR>=N {printf "%s\n",sum; N+=3; sum=0}
{sum+=$1}...

As you're only dealing with one column, and working with consecutive numbers it's a lot simpler:
awk '{sum+=$1} NR%3==0{print sum; sum=0}' file

The logic you describe and the sample you give do not coincide. Anyhow, using 6 as the delta to increase your field 1 counter, tryawk 'NR==1 {printf "%s\t",$1; N=$1+6}
$1>=N ...

For not too large files, try:grep -v "$(cut -d" " -f1,2 file2)" file1
sc2/10 10 . G C 50 F=5;U=4
sc2/24 24 . T G 31 F=5;U=4
sc2/11 30 . A T 60 F=5;U=4

awk 'NR==FNR{a[$1 FS $2];next} !($1 FS $2 in a)' file2 file1

sc2/10 10 . G C 50 F=5;U=4
sc2/24 24 . T G 31 F=5;U=4
sc2/11 30 . A T 60 F=5;U=4

Try:
awk 'NR==FNR{A[$1,$2,$4]=$0; A[$1,$2,$5]=$0; next} $4==$5 && ($1,$2,$4) in A {print A[$1,$2,$4] ";" $0}' file1 file2

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i want to print ODD lines like first ,third then fifth and so on


234,567,ABC,KJL
234,565,ABD,KJL
234,568,ABE,KJL
234,560,ABF,KJL
234,563,ABG,KJL
234,562,ABH,KJL

O/P will be like...