Closed Adeel3Dgenomics closed 1 month ago
Hi all,
i am trying to impute a sample data set, and it continuously giving me this error. i have my_study.bim, .bed and .fam
"More than 100 allele switches have been detected. Imputation cannot be started!"
data preparation commands are as follows.
plink --freq --bfile my_study --out my_study perl HRC-1000G-check-bim.pl -b my_study.bim -f my_study.frq -r HRC.r1-1.GRCh37.wgs.mac5.sites.tab -h sh Run-plink.sh plink --bfile my_study-updated-chr3 --recode vcf --out my_study_chr3 vcf-sort my_study-chr3.vcf| bgzip -c > my_study-chr3.vcf.gz
Hi all,
i am trying to impute a sample data set, and it continuously giving me this error. i have my_study.bim, .bed and .fam
"More than 100 allele switches have been detected. Imputation cannot be started!"
data preparation commands are as follows.