How to choose --mind value for plink SNPs filtering

Question

[anithanagaraj93]

I am trying to filter SNPs after converting vcf to plink format of only bialleleic SNPs, So itried following steps:

1. plink --bfile idfilled_data --geno 0.1 --maf 0.1 --allow-extra-chr --make-bed --out maf_filtered_data
2. plink2 --bfile maf_filtered_data --allow-extra-chr --indep-pairwise 200kb 1 0.15 --out ldpruned_snplist
3. plink --bfile maf_filtered_data --extract ldpruned_snplist.prune.in
4. plink --bfile ldpruned_data --allow-extra-chr --pca --out pca_results

After 1st step got Total genotyping rate is 0.954895 and continued upto 4th step, without using --mind, throws an error. So in the filtering how can I use --mind value? is it same Total genotyping rate is 0.954895 need to consider? because value looks very high.

Please help me out to solve this issue.

Thanks

[Fabio Marroni]

Did the error message mention --mind? And how many individuals are in your data set? According to the manual you should set --mind to the maximum allowed fraction of missing values per individual. You may try 0.1 as shown in the manual.