Question: vcf to plink format
1
gravatar for natasha
4.0 years ago by
natasha100
natasha100 wrote:

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

plink vcf • 3.2k views
ADD COMMENTlink modified 3.8 years ago by Biostar ♦♦ 20 • written 4.0 years ago by natasha100

Were homozygous reference SNPs removed?

ADD REPLYlink written 4.0 years ago by andrew.j.skelton736.0k

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?

ADD REPLYlink written 4.0 years ago by natasha100

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

ADD REPLYlink written 4.0 years ago by andrew.j.skelton736.0k

This post may be helpful.

How To Convert Vcf File To Plink Ped Format?

especially the answer in the end.

ADD REPLYlink modified 3.8 years ago • written 3.8 years ago by natasha.sernova3.7k

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.

ADD REPLYlink written 3.8 years ago by vakul.mohanty240
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