How to choose –mind value for plink SNPs filtering

How to choose –mind value for plink SNPs filtering

0

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


SNPs


mind


plink


filter

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