I have files with the 2504 individuals of the 1000 genomes project, and I want to filter by population. I did the following for the first population (ACB):
plink --file all1000gen --keep indACB.txt --make-bed --out all1000genACB
but it gives back the following error:
Error: Line 1 of --keep file has fewer tokens than expected.
my indACB.txt file looks like this:
head indACB.txt HG01879 HG01880 HG01882 HG01883 HG01885 HG01886 HG01889 HG01890 HG01894 HG01896
which I made (por each population, using grep) from the population information file that's available in the 1000 genomes page, which has a two times the individual ID (first two columns) and one with the population name, as shown:
head indpop2.txt HG00096 HG00096 GBR HG00097 HG00097 GBR HG00099 HG00099 GBR HG00100 HG00100 GBR HG00101 HG00101 GBR HG00102 HG00102 GBR HG00103 HG00103 GBR HG00105 HG00105 GBR HG00106 HG00106 GBR HG00107 HG00107 GBR
I think there's a problem with my --keep file, but I'm not sure what's the wanted structure of the txt file.
I also tried greping ACB individuals from indpop2.txt , so the new indACB.txt file looks like this:
head indACB2.txt HG01879 HG01879 ACB HG01880 HG01880 ACB HG01882 HG01882 ACB HG01883 HG01883 ACB HG01885 HG01885 ACB HG01886 HG01886 ACB HG01889 HG01889 ACB HG01890 HG01890 ACB HG01894 HG01894 ACB HG01896 HG01896 ACB
But it yields the following error:
plink --file allconcat39 --keep indACB2.txt --make-bed --out allconcat43ACB Error: No people remaining after --keep.