Entering edit mode
8.3 years ago
natasha
▴
110
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
Were homozygous reference SNPs removed?
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?
If it's homozygous to the reference, does not mean that by definition, it isn't a SNP?
This post may be helpful.
How To Convert Vcf File To Plink Ped Format?
especially the answer in the end.
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.