vcf to plink format
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5.1 years ago
natasha ▴ 100

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

vcf plink • 4.1k views
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Were homozygous reference SNPs removed?

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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?

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

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This post may be helpful.

How To Convert Vcf File To Plink Ped Format?

especially the answer in the end.

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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.

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