vcf to plink format

Question

[natasha]

Hi

I have used the following command;

vcftools --vcf < input.vcf> --plink --out < output>

My vcf file contained the location of 7030 SNPs, however my .ped file now only contains 6800, why is this?

Thanks

[andrew.j.skelton73]

Were homozygous reference SNPs removed?

[natasha]

Yes... however I am dealing with a haploid organism and I want all SNPs to be included. IS there a way in which I can do this?

[andrew.j.skelton73]

If it's homozygous to the reference, does not mean that by definition, it isn't a SNP?

[natasha.sernova]

This post may be helpful.

How To Convert Vcf File To Plink Ped Format?

especially the answer in the end.

[vakul.mohanty]

One possibility could be that some SNPs fail the MAF filter. You can also make the conversion using plink 1.9 plink --vcf vcf_name --make-bed --out name (https://www.cog-genomics.org/plink2/data) this will give you files in the plink bed format.