CODEWITHSUNDEEP
awk
justaguy
justaguy

Reputation: 3022

awk not printing header in output file

The below awk seems to work great with 1 issue, the header lines do hot print in the output? I have been staring at this awhile with no luck. What am I missing? Thank you :).

awk

awk 'NR==FNR{for (i=1;i<=NF;i++) a[$i];next} FNR==1 || ($7 in a)' /home/panels/file1 test.txt | 
awk '{split($2,a,"-"); print a[1] "\t" $0}' | 
sort | 
cut -f2-> /home/panels/test_filtered.vcf

test.txt (used in the awk to give the filtered output --only a small portion of the data but the tab delimited format is shown)

Chr Start   End Ref Alt
chr1    949608  949608  G   A

current output (has no header)

chr1    949608  949608  G   A

desired output (has header)

Chr Start   End Ref Alt
chr1    949608  949608  G   A

Upvotes: 1

Views: 357

Answers (2)

karakfa
karakfa

Reputation: 67507

you can combine your scripts and add the sort into awk and handle header this way.

$ awk 'NR==FNR{for(i=1;i<=NF;i++)a[$i]; next} 
        FNR==1{print "dummy\t" $0; next}
       $7 in a{split($2,b,"-"); print b[1] "\t" $0 | "sort" }' file1 file2 |
  cut -f2

Upvotes: 0

William Pursell
William Pursell

Reputation: 212404

It looks like the header is going to sort, and getting mixed in with your data. A simple solution is to do:

... | { read line; echo $line; sort; } |

to prevent the first line from going to sort.

Upvotes: 2

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