awk to compare each file in two directores by storing in variable
In the below bash I am trying to read each file from a specific directory into a variable REF or VAL. Then use those variables in an awk to compare each matching file from REF and VAL. The filenames in the REF are different then in the VAL, but have a common id up until the _ I know the awk portion works as I can run files through them manually. However, I am not sure if I am doing the variable part correctly. Thank you .
The two variables are:
REF comes from /home/cmccabe/Desktop/comparison/reference/10bp and is 3 files:
VAR comes from /home/cmccabe/Desktop/comparison/validation/files and is 3 files:
So, S1234_ref.txt would be REF and S1234_panel.vcf would be VAL, then those two files would be compared. I think I am close but not too sure about the variables.
Last edited by cmccabe; 09-30-2016 at 04:01 PM..
Reason: added details
HI
I am trying to store the output of this awk command
awk -F, {(if NR==2) print $1} test.sr
in a variable when I am trying v= awk -F, {(if NR==2) print $1} test.sr
$v = awk -F, {(if NR==2) print $1} test.sr
but its not working out .
Any suggestions
Thanks
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