I have a GWAS sumstats file called sumstats.txt in the following format:
SNP Freq.A1 CHR BP A1 A2 OR SE P
10:100968448:T:AA 0.3519 10 100968448 t aa 1.0024 0.01 0.812
10:101574552:A:ATG 0.4493 10 101574552 a atg 0.98906 0.0097 0.2585
10:10222597:AT:A 0 10 10222597 a at 0.9997 0.01 0.9777
For every entry in the sumstats file I need to munge column 1 to retain only the chromosomal information, effectively deleting everything after the first colon, whilst leaving the rest of the file intact.
The final file would look like this:
SNP Freq.A1 CHR BP A1 A2 OR SE P
10 0.3519 10 100968448 t aa 1.0024 0.01 0.812
10 0.4493 10 101574552 a atg 0.98906 0.0097 0.2585
10 0 10 10222597 a at 0.9997 0.01 0.9777
My awk/sed knowledge is not great but I've had a bash (npi!!):
echo "10:100968448:T:AA 0.3519 10 100968448 t aa 1.0024 0.01 0.812" | awk '{n=split($0,a,/[:_]/); print a[1]"\t"a[2]"\t"a[2]+1"\t"a[3]"/"a[4];}'
Giving:
10 100968448 100968449 T/AA 0.3519 10 100968448 t aa 1.0024 0.01 0.812
But not sure how to get rid of the info after the colon and pipe the file in correctly. Also tried:
echo "10:100968448:T:AA 0.3519 10 100968448 t aa 1.0024 0.01 0.812" | awk '{n=split($0,a,/[:_]/); print a[1];}'
Returning:
10
I'm looking for a bash/awk/sed one liner for this as I have quite a few sumstats files to process.
Any suggestions would be greatly appreciated.
•
written
by
camerond
2 answers
It looks like your goal is to split the first field on the colon, then print the rest of the file. Your awk script is splitting the line not the field. You can try:
awk 'BEGIN{OFS="\t";FS="\t"} {split($1,ARR,":"); $1 = ARR[1]; print $0}' inFile.txt > outFile.txt
This will yield:
SNP Freq.A1 CHR BP A1 A2 OR SE P
10 0.3519 10 100968448 t aa 1.0024 0.01 0.812
10 0.4493 10 101574552 a atg 0.98906 0.0097 0.2585
10 0 10 10222597 a at 0.9997 0.01 0.9777
The awk script is doing a few things:
BEGIN{OFS="\t";FS="\t"} is defining the Output Field Separator and Field Separator as tabs.
split($1,ARR,":") splits just the first field on the colon, and stores each element in the array ARR
$1 = ARR[1] redefines the first field as the first array element (just the chromosome in this case).
print $0 prints the entire line (with the newly defined first field).
something like this ?
sed 's/^\([^:]*\):[^ \t]*/\1\t/'
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