SEQanswers (
-   Bioinformatics (
-   -   plink files to vcf conversion (

Vanisha 11-29-2011 02:20 AM

plink files to vcf conversion
Is there anyway to convert plink (.map,.ped) files back to vcf?

I originally converted vcf to plink format files using vcftools, applied some QC in plink and now want to call the QC'd variants using Annovar - however Annovar doesn't accept plink file format, or does it? I can't see on website. Any help/advice is appreciated


nilshomer 11-29-2011 04:29 PM

Looks like the Broad may have a solution:

emilyjia2000 12-26-2011 05:31 AM

Hi Vanisha,

How did you convert VCF to PED using Vcftools? I tried it, but it generated error. I really appreciate your help.


emilyjia2000 12-26-2011 06:43 AM

I converted from VCF to PED format, but when I looked at the PED file, it didn't show which samples are affected or unaffected? I only got two files from the conversion, PED and MAP, I still need datfile to use in the linkage, anyone knows about it?
Thanks a lot,

Vanisha 01-03-2012 12:46 AM

you can update phenotype in plink (--pheno) and you may have to make you're own .dat file for the linkage - sorry don't know much more

bpb9 02-19-2013 04:16 AM

I am also trying to convert a VCF file to plink format using vcftools, but the process never seems to result in a plink file. For example when I enter:

./vcftools --vcf filename.vcf --plink

I see:

VCFtools - v0.1.9.0
(C) Adam Auton 2009

Parameters as interpreted:
--vcf filename.vcf

Reading Index file.
Building new index file.
Scanning Chromosome: chr1
Warning - file contains entries with the same position. These entries will be processed separately.

Scanning Chromosome: chr2
Scanning Chromosome: chr3
Scanning Chromosome: chr4
Scanning Chromosome: chr5
Scanning Chromosome: chr6
Scanning Chromosome: chr7
Scanning Chromosome: chr8
Scanning Chromosome: chr9
Scanning Chromosome: chr10
Scanning Chromosome: chr11
Scanning Chromosome: chr12
Scanning Chromosome: chr13
Scanning Chromosome: chr14
Scanning Chromosome: chr15
Scanning Chromosome: chr16
Scanning Chromosome: chr17
Scanning Chromosome: chr18
Scanning Chromosome: chr19
Scanning Chromosome: chr20
Scanning Chromosome: chr21
Scanning Chromosome: chr22
Scanning Chromosome: chrX
Scanning Chromosome: chrY
Writing Index file.
File contains 11725221 entries and 30 individuals.
Applying Required Filters.
After filtering, kept 30 out of 30 Individuals
After filtering, kept 11725221 out of a possible 11725221 Sites
Writing PLINK PED file ...
PLINK: Only outputting biallelic loci.
Segmentation fault: 11

What is segmentation fault: 11 ? Is it the reason there is not a plink file output at the end of this process? Also, do I need to do something differently in order for this command to actually result in a plink files rather than a vcf?

Many thanks...

Vanisha 02-19-2013 04:23 AM

Try this:
--vcf file.vcf --out file.plink --plink

However, it might be better instead of converting vcf to plink and then doing plink analysis, just use vcftools to do the plink QC; the format will still be VCF, and then use the QC'd VCF to perform any downstream analysis

bpb9 02-19-2013 05:05 AM

Thanks for the tips!

bpb9 02-19-2013 11:10 AM

After having made the plink files from the VCF file, I tried to split them up by chromosome in plink but encountered the following error:

ERROR: Locus has >2 alleles:
individual has genotype [ G 0 ]
but we've already seen [ G ] and [ A ]

I thought 0 indicated a monomorphic SNP. I am very confused. I suppose I could try splitting up the vcf file by chromosome in vcftools and then converting to plink, but I don't see why that would get around the above issue. Would it help to recode only biallelic SNPs to plink format instead of all biallelic loci? Is there a way to do that? Any input is appreciated!

sukesh14 09-20-2016 11:38 PM

I would like to convert bed to vcf .. I tried using plink.. i could not follow the tutorial.. Can anyone help me


rajeshkmaurya08 03-13-2017 10:48 PM

Its is again showing warning like:

plink: unknown option "--file"
plink: unknown option "--make-bed"

All times are GMT -8. The time now is 09:05 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.