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Question: Convert VCFf file to plink ped/map format while filtering the SNPs
7
gravatar for roll
6.3 years ago by
roll • 330
United Kingdom
roll • 330 wrote:

Hi,

I was working on converting my vcf file into plink ped/map format.

I used the following command from vcftools

vcftools --vcf myvcf.vcf --plink --out myplink

I also would like to filter my snps based on minor allele frequency (maf).

I was wondering whether simply using

vcftools --vcf myvcf.vcf --plink --maf 0.05 --out myplink

would do it in one step?

Or shall i do it in two steps. First convert it to the ped/map format and then use plink to do the filtering?
vcftools ped map plink • 33k views
ADD COMMENT • link •
modified 23 months ago by hakimeazarafra • 0 • written 6.3 years ago by roll • 330
10
gravatar for chrchang523
6.3 years ago by
chrchang523 ♦ 7.6k
United States
chrchang523 ♦ 7.6k wrote:

PLINK 1.9 can do this:

plink --vcf myvcf.vcf --maf 0.05 --recode --out myplink

(Are you sure you want to convert to ped/map, though? PLINK prefers to work with binary bed/bim/fam.)
ADD COMMENT • link modified 2.2 years ago by zx8754 ♦ 9.9k • written 6.3 years ago by chrchang523 ♦ 7.6k

Hi, could you please explain what information will be written to .fam file since vcf file will not have that informtion (as per my understanding)? Can we append information to .fam file later?

ADD REPLY • link written 9 months ago by enigmargs • 0
0
gravatar for hakimeazarafra
23 months ago by
hakimeazarafra • 0
hakimeazarafra • 0 wrote:

Hi I am new user in PLINK and I have a problem. I have a vcf file (by this command plink --vcf myfile.vcf --allow-no-samples --make-bed --out newphase) it converted to bed /bim and fam files. now I would like to get minor allele frequency of this file (with this command plink --bfile newphase --freq --make-bed --out newphase-frq) but I get this error the fam file is empty. what should i do? is there any way which i can get minor allele frequency of my bed file by plink?
ADD COMMENT • link written 23 months ago by hakimeazarafra • 0

I think you need samples in your vcf to calculate the minor allele frequency. If you are using --allow-no-samples your vcf might have no samples to calculate it from.

ADD REPLY • link written 23 months ago by Raony Guimarães • 1.1k
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