vcf file filtration w.r.t. missingness per snps and unmapped snps

Question

[analyst]

Hi,

I have wheat hexaploid merged vcf file and I have to filter vcf w.r.t missingness per snp 50%, unmapped snps to remove, and heterozygous snps below 0.2 threshold to remove using bcftools or any other tool because plink is not supported for polyploid data.

Kindly provide your valuable suggestions.

[Pierre Lindenbaum]

unmapped snps

what is an unmapped snps ?

[analyst]

I am following this paper. Here it is mentioned under Genotyping and Quality Control section of Material and Methods.

[Pierre Lindenbaum]

what is w.r.t ?

[analyst]

with respect to