I open a forum to record frequently problem I met in the genetic data analysis. Just come to this field and find lots of interesting things to share.

1. Some SNP have multiple genomic positions, maybe in same chromosome or different chromosome. For example, rs10408018 located in chr19: 41543327 and chrX: 67106620. These specific SNPs will bring lots of troubles for plink analysis. (since plink don't allow non-unique rsid for the anlayisis pipeline). Solution: remove any one of the repeated SNPs with --exclude. and be careful, missnp result sometimes start with a special . in the first line, remove it before use --exclude
2. vcf format files derived from NGS will have genotypes like ./. and ./0, it will make plink stop running, remove such genotype from vcf files. Plink is used to deal with genotyping data from microarray, not sequencing data.