How to choose –mind value for plink SNPs filtering
I am trying to filter SNPs after converting vcf to plink format of only bialleleic SNPs, So itried following steps:
- plink –bfile idfilled_data –geno 0.1 –maf 0.1 –allow-extra-chr –make-bed –out maf_filtered_data
- plink2 –bfile maf_filtered_data –allow-extra-chr –indep-pairwise 200kb 1 0.15 –out ldpruned_snplist
- plink –bfile maf_filtered_data –extract ldpruned_snplist.prune.in
- 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
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