VCF file generation from multiple samples fro PCA

Question

[Aruna]

I am trying to generate vcf file for 80 samples(human) and use it for pca. But when trying to get eigen vectors using plink it says genotyping rate is 0.12 and when i remove snps with missing data threshold all data is removed. i dont know where i am making mistake.

samtools mpileup --skip-indels -d 250 -m 1 -E --BCF --output-tags DP,DV,DP4,SP -f <reference genome.fa> -o <output.bcf> <list of input bam files>
bcftools index  <output.bcf> <indexed.bcf>
bcftools call --skip-variants indels --multiallelic-caller --variants-only  -O v <output.bcf> -o <output.vcf>