Empty Valid SNP ID

[science987]

Dear author,

I am having some problems with using PRSice. I get an error saying duplicated SNP id:

Error: A total of 1 duplicated SNP ID detected out of 0
input SNPs! Valid SNP ID (post --extract /
--exclude, non-duplicated SNPs) stored at
lee_PRSice.valid. You can avoid this error by using
--extract lee_PRSice.valid

However this '.valid' file is empty. Consequently when I try to use --extract or --exclude in my code it does not work. I read on previous posts that updating to latest software might help for this. I have updated the PRSice download to 2.3.5 as per the website but get the same problem.

I have tried to use the awk command as found in your post in 'issue 270' but that has not seemed to work as I still get an empty valid file :
awk '!($1 in a) {a[$1] = 1; print;}' lee_corrected.txt > lee_corrected_nodup

Rscript PRSice.R --dir . --prsice PRSice_linux --base lee_corrected.txt --target trial2 --thread 1 --stat beta.column --beta --binary-target T --chr chr --A1 allele_A --A2 allele_B --pvalue P_value --chr-id íd --out lee_PRSice

The code goes through to 100% then gives out the error of duplicated SNP ID with an empty .valid file

I would appreciate any advise as I would like to try to use this for my work

Many Thanks,