Extract rows present in file1 and not in file 2

Question

[ijlal.hyder2012]

Hello everyone,

I have 2 tab separated files and I want to compare them on the basis of chr,start,ref and alt and print only the rows of file1 that aren't present in file2 in the output file. please see below.

file1:

chr start   ref alt freq
1   11906040    C   T   2.76E-05
1   11906049    C   T   2.76E-05
1   11906068    A   G   0.147142
1   11907124    C   T   2.77E-05
1   11907125    C   G   0.000471777
1   11907703    AAGG    A   2.78E-05
1   11907717    CGGT    C   5.59E-05

File2:

chr start      end  ref   alt    freq
1       12198   12198   G       C       .
1       12237   12237   G       A       .
1       12259   12259   G       C       .
1       12266   12266   G       A       .
1       12746   12773   GGGAGTGGCGTCGCCCCTAGGGCTCTAC    -       0
1       12745   12773   TGGGAGTGGCGTCGCCCCTAGGGCTCTAC   T       0
1   11907703    AAGG    A   2.78E-05
1   11907717    CGGT    C   5.59E-05

output file:

chr start   ref alt freq
1   11906040    C   T   2.76E-05
1   11906049    C   T   2.76E-05
1   11906068    A   G   0.147142
1   11907124    C   T   2.77E-05
1   11907125    C   G   0.000471777

thanks in advance.

Regards,

Answer 1

[AK]

From your example inputs and output, it can also be:

$ grep -v -f file2.tab file1.tab
chr     start   ref     alt     freq
1       11906040        C       T       2.76E-05
1       11906049        C       T       2.76E-05
1       11906068        A       G       0.147142
1       11907124        C       T       2.77E-05
1       11907125        C       G       0.000471777

But only if the format in your file2 is correct, since the last two rows in your file2 are with 5 fields, not 6 (no end).

$ awk '{print NF}' file2.tab
6
6
6
6
6
6
6
5
5

Answer 2

[ATpoint]

Look at bedtools intersect and the -v option.