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I am trying to find this pattern on a large file but the output doesn't look good. The output doesn't seem to reflect the pattern.

Father = 1|0 or 1/0

Mother = 110 or 1/0

Daughter 1 = 1|0 or 1/0

Daughter 2 = 1|1 or 1/1

Daughter 3 = 0|0 or 0/0

Son 1 = 1|0 or 1/0

Son 2 = 1|1 or 1/1

The content of the file1 looks like this

CHROM   POS REF ALT FATHER  MOTHER  DAUGHTER1   DAUGHTER2   DAUGHTER3   

SON1    SON2    INFO    FREQUECY
1   1226852 G   C   1/0 0/0 1|0 1|0 1|0 1|0 0|0 AN=2184;AC=12   0.005494505
1   1847936 C   T   0/1 1/1 1|1 1|1 1|1 1|1 0|1 AC=1;AN=2184    0.000457875
1   2428427 C   G   0/1 0/0 0|0 0|0 0|0 0|0 1|0 AC=4;AN=2184    0.001831502
1   2515616 G   A   1/0 1/0 1/0 1|1 1|1 1/0 1/0 AC=1;AN=2184    0.000457875
1   3801895 T   C   1/0 1/0 0|0 1/0 1/0 0|0 1|1 AC=10;AN=2184   0.004578755
1   3833321 T   C   1/0 1/0 1|1 1/0 1/0 1|1 0|0 AN=2184;AC=801  0.366758242
1   9009352 A   G   0/1 0/1 1|1 0/1 0/1 1|1 0|0 AC=90;AN=2184   0.041208791
1   9328077 G   A   1/1 0/0 1|0 1|0 1|0 1|0 1|0 AC=1;AN=2184    0.000457875
1   10684412    C   T   0/1 0/0 1|0 1|0 1|0 1|0 0|0 AN=2184;AC=2    0.000915751
1   11782120    G   A   1/0 0/0 0|0 0|0 1|0 1|0 0|0 AC=3;AN=2184    0.001373626
1   12034879    A   T   0/1 1/1 0|1 0|1 0|1 0|1 1|1 AC=3;AN=2184    0.001373626
1   16064465    C   A   1/0 0/0 0|0 0|0 0|0 0|0 1|0 AN=2184;AC=4    0.001831502
1   16111170    G   A   1/0 1/0 1/0 0|0 0|0 1/0 1/0 AC=1;AN=2184    0.000457875
1   16200229    C   A   0/0 1/0 0|0 0|1 0|1 0|0 0|1 AC=9;AN=2184    0.004120879
1   16258118    C   T   0/1 0/0 1|0 1|0 1|0 1|0 0|0 AN=2184;AC=1    0.000457875
1   17966719    A   G   0/0 0/1 0|1 0|0 0|0 0|1 0|0 AC=0;AN=2184    0
1   19751079    CG  C   0/1 0/1 1|1 0|0 0|0 0/1 0/1 AN=2184;AC=1    0.000457875
1   19955045    G   A   0/0 1/0 0|0 0|1 0|1 0|0 0|1 AN=2184;AC=4    0.001831502
1   21060356    G   A   1/0 1/0 1/0 1/0 1/0 1|1 0|0 AN=2184;AC=541  0.247710623

My awk script look like this

awk '($8~/1\/1/ || $8~/1\\|1/) && ($9~/0\/0/ ||$9~/0\\|0/) && ($7~/^1\\|0/||$7~/1\/0/) && ($10~/1\\|0/||$7~/1\/0/) && ($10~/0\/0/ ||  $10~/0\\|0/) && ($5~/1\/0/|| $5~/1\\|0/) && ($11~/0\/1/||$11~/0\\|1/)&& ($6~/1\\|0/||$6~/1\/0/) && ($12 ~/1\/1/ ||12~/1\\|1/){print}' file1 >file2
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  • $\begingroup$ What's wrong with the output? "Doesn't look good" isn't very informative. Please edit your question and highlight what is going wrong. $\endgroup$ – terdon Oct 9 '19 at 8:20
  • $\begingroup$ The output doesn't reflect the pattern. $\endgroup$ – user11766958 Oct 9 '19 at 8:37
  • $\begingroup$ Well yes, I imagine so. But since this is a really complex pattern, it would be very helpful if you could show the output you get and explain why it is wrong. I wrote you the script you're using, and I still don't see what the issue is. $\endgroup$ – terdon Oct 9 '19 at 8:40
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Example output of what you got and what you expected would be helpful, without these one can only guess.

First of all your input does not have a row satisfying the criteria you have given, so I added two dummy rows, one with / and one with | used as separator.

Here is the code I used:

awk '($5~/1\|0/ || $5~/1\/0/) && ($6~/1\|0/ || $6~/1\/0/) && ($7~/1\|0/ || $7~/1\/0/) && ($8~/1\|1/ || $8~/1\/1/) && ($9~/0\|0/ || $9~/0\/0/) && ($10~/1\|0/ || $10~/1\/0/) && ($11~/1\|1/ || $11~/1\/1/) {print}' test.txt

And its output (input is yours + 2 dummy rows):

Dummy  dummy D D 1/0 1/0 1/0 1/1 0/0 1/0 1/1 dummy dummy
Dummy  dummy D D 1|0 1|0 1|0 1|1 0|0 1|0 1|1 dummy dummy

The code is basically yours, except for:

  • I escaped | with one \ instead of two
  • I changed this part: ($10~/1\\|0/||$7~/1\/0/). I think $7 should have been $10
  • I removed a ^ from one of your conditions, I believe they all should start with ^ though, per @terdon's answer on a related question

I believe the code above does what you want, but when I run code above with two backslashes to escape I get the following output and could not figure out why!

1   3801895 T   C   1/0 1/0 0|0 1/0 1/0 0|0 1|1 AC=10;AN=2184   0.004578755
1   16200229    C   A   0/0 1/0 0|0 0|1 0|1 0|0 0|1 AC=9;AN=2184    0.004120879
1   19955045    G   A   0/0 1/0 0|0 0|1 0|1 0|0 0|1 AN=2184;AC=4    0.001831502
Dummy  dummy D D 1/0 1/0 1/0 1/1 0/0 1/0 1/1 dummy dummy
Dummy  dummy D D 1|0 1|0 1|0 1|1 0|0 1|0 1|1 dummy dummy
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