Printing and separating columns in awk

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I have file (VCF) as like this

##fileformat=VCFv4.0
##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FILTER=<ID=q10,Description="Quality below 10">
##FILTER=<ID=s50,Description="Less than 50% of samples have data">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
#CHROM POS     ID        REF ALT    QUAL FILTER INFO    FORMAT      NA00001
Chr02   259 .   A   .   20  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:1:0,1:0,0:0,0:0,0:0,26,23,75,33,33,33,47,52,49:23
Chr02   260 .   C   .   13  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:1:0,0:0,1:0,0:0,0:24,0,70,17,25,49,43,25,25,44:16
Chr02   261 .   C   .   13  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:1:0,0:0,1:0,0:0,0:24,0,194,18,25,49,44,25,25,45:16
Chr02   262 .   C   A   21  .   .   GT:DP:A:C:G:T:PP:GQ 0/1:1:0,0:0,1:0,0:0,0:387,0,342,348,25,368,376,25,25,368:25
Chr02   263 .   C   .   24  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:2:0,0:1,1:0,0:0,0:541,0,529,495,29,556,508,29,29,499:29
Chr02   264 .   A   .   31  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:2:1,1:0,0:0,0:0,0:0,280,192,317,36,36,36,178,302,219:36
Chr02   265 .   G   C   25  .   .   GT:DP:A:C:G:T:PP:GQ 0/1:2:0,0:0,0:1,1:0,0:255,414,0,328,284,29,284,29,351,29:29
Chr02   266 .   A   .   31  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:2:1,1:0,0:0,0:0,0:0,281,323,440,36,36,36,209,309,315:36
Chr02   267 .   C   .   24  .   .   GT:DP:A:C:G:T:PP:GQ 0/0:2:0,0:1,1:0,0:0,0:595,0,541,481,28,567,512,28,28,512:

And I just need to print first and second row as like this

 Chr02:259-259
 Chr02:260-260
 Chr02:261-261
 Chr02:262-262
 Chr02:263-263
 .
 .
 .
 Chr02:267-267

I have tried with this command in awk

awk '{ OFS = ":" }{print$1,$2,$2}' input.txt

But it is not worked for me

awk
1 Answers

Could you please try following, written and tested with shown samples only in GNU awk.

awk '/^Chr/{print $1":"$2"-"$2}' Input_file

OR in case you want to look for lines which are starting with Chr followed by digits then try following.

awk '/^Chr[0-9]+/{print $1":"$2"-"$2}' Input_file

OR in case you want to leave only commented lines then try following:

awk '!/^#/{print $1":"$2"-"$2}' Input_file

Explanation: Simply checking condition if line starts from Chr(in first solution) OR Chr followed by digits(in 2nd solution) OR line doesn't start from #(3rd solution) then print 1st field colon 2nd field dash 2nd field.

user_58665800
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