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Old 11-29-2011, 02:20 AM   #1
Vanisha
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Default 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

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Old 11-29-2011, 04:29 PM   #2
nilshomer
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Looks like the Broad may have a solution: http://www.broadinstitute.org/gsa/wi...ing_ped_to_vcf

Last edited by nilshomer; 11-29-2011 at 05:51 PM.
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Old 12-26-2011, 05:31 AM   #3
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Hi Vanisha,

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

Thanks
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Old 12-26-2011, 06:43 AM   #4
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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,
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Old 01-03-2012, 12:46 AM   #5
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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
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Old 02-19-2013, 04:16 AM   #6
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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
--plink

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...
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Old 02-19-2013, 04:23 AM   #7
Vanisha
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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
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Old 02-19-2013, 05:05 AM   #8
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Thanks for the tips!
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Old 02-19-2013, 11:10 AM   #9
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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!
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Old 09-20-2016, 11:38 PM   #10
sukesh14
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I would like to convert bed to vcf .. I tried using plink.. i could not follow the tutorial.. Can anyone help me

Thanks
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Old 03-13-2017, 10:48 PM   #11
rajeshkmaurya08
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Its is again showing warning like:

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