Question: Convert VCFf file to plink ped/map format while filtering the SNPs
7
gravatar for roll
5.9 years ago by
roll320
United Kingdom
roll320 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 • 31k views
ADD COMMENTlink modified 17 months ago by hakimeazarafra0 • written 5.9 years ago by roll320
9
gravatar for chrchang523
5.9 years ago by
chrchang5237.1k
United States
chrchang5237.1k 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 COMMENTlink modified 20 months ago by zx87549.4k • written 5.9 years ago by chrchang5237.1k

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 REPLYlink written 4 months ago by enigmargs0
0
gravatar for hakimeazarafra
17 months ago by
hakimeazarafra0 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 COMMENTlink written 17 months ago by hakimeazarafra0

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 REPLYlink written 17 months ago by Raony GuimarĂ£es1.1k
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