Filtering a large file based on a specific column in bash

Question

Filtering a large file based on a specific column in bash

I have a file with lines> 100m and you want to filter it by some criteria:

$ wc -l s1bam.bed 
104797540 s1bam.bed

$ head -n 3 s1bam.bed 
chr1    14688   14979   NB501800:50:H3NW5BGX3:2:22310:19560:5036/1  3   +
chr1    14688   14979   NB501800:50:H3NW5BGX3:3:13501:3458:17919/1  3   +
chr1    14727   15018   NB501800:50:H3NW5BGX3:2:22310:19560:5036/2  3   -

What I wanted to output is the fifth field value >=20

and !=255

(for example, the second field from the right). How do I implement it in Bash?

+3

bash

David Z Jul 20. 17 at 14:26

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1 answer

anubhava · Accepted Answer · 2017-07-20T14:31:27+0000

You can use awk for this:

awk '$5 >= 20 && $5 != 255' file

Filtering a large file based on a specific column in bash

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