CODEWITHSUNDEEP
bashunixawk
MrFronk
MrFronk

Reputation: 392

extracting whole line in awk if condition using cut -d

I want to get the value of the 11th column in my tab delimited file. This return value is multiple values concetenated using : as seperator.

example result from cat myFile | cut -d':'    :
.:7:.:2:100:.

I now want to split this file on the : seperator and retrieve the second value. This can be done with cut -d':' -f2

my question: How can I make a statement which returns all lines in my file which have value 5 or more in the second part of the 11th column?

input file (2 lines):

chr1    4396745 bnd_549 a   a[chr9:136249370[   100 PASS    SVTYPE=BND;MATEID=bnd_550;EVENT=transl_inter_1022;GENE=;    GT:AD:DP:SS:SSC:BQ  .:.:.:.:.:. .:7:.:2:100:.
chr1    6315381 bnd_551 c   ]chr9:68720182]c    100 PASS    SVTYPE=BND;MATEID=bnd_552;EVENT=transl_inter_9346;GENE=;    GT:AD:DP:SS:SSC:BQ  .:.:.:.:.:. .:3:.:2:100:.

expected output:

chr1    4396745 bnd_549 a   a[chr9:136249370[   100 PASS    SVTYPE=BND;MATEID=bnd_550;EVENT=transl_inter_1022;GENE=;    GT:AD:DP:SS:SSC:BQ  .:.:.:.:.:. .:7:.:2:100:.

output with (awk -F: '$11>=5' example.sorted.vcf): no output

Upvotes: 2

Views: 584

Answers (2)

glenn jackman
glenn jackman

Reputation: 247042

You could also use whitespace or colon as the field separator:

awk -F ':|[[:blank:]]+' '$23 > 5' filename

Upvotes: 0

jaypal singh
jaypal singh

Reputation: 77145

This should work (though untested, please provide input and expected output): 

awk '{split($11,ary,/:/); if(ary[2]>=5) print}' myFile

Upvotes: 4

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