I do have a dataset in Eigenstrat format and I did compute stats using it.
Now I want to compute the same stats on the autosomal chromosomes and hence I am trying to remove chromosome X - Y (i.e. 23 and 24 in the .snp file).
I did remove those SNPs locations from those chromosomes in the .snps file but when I try to compute any stats (in admixr) I do have this error:
OOPS number of SNPs 1150639 != 1233013 in input file: v42.4.1240K.geno
I do understand this, pretty much means that I didn't remove those SNPs from the .geno file at each location.
However I do not know how to remove those easily from the .geno file ? I could rerun the calling step to generate a dataset without those location but do you know any easier way ?