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Old 11-28-2012, 07:29 AM   #1
pepsimax
Junior Member
 
Location: London

Join Date: May 2012
Posts: 9
Default vcf to plink format conversion problems

I have two vcf's that I want to convert to plink format. Running:
Code:
vcftools --gzvcf chr_10.flt.vcf.gz --plink-tped

VCFtools - v0.1.8
(C) Adam Auton 2009

Parameters as interpreted:
	--gzvcf chr_10.flt.vcf.gz
	--plink-tped

Using zlib version: 1.2.3
Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
VCF index is older than VCF file. Will regenerate.
Building new index file.
Writing Index file.
File contains 0 entries and 364 individuals.
Applying Required Filters.
After filtering, kept 364 out of 364 Individuals
After filtering, kept 0 out of a possible 0 Sites
Error:No data left for analysis!
and the error on the second:

Code:
 vcftools --gzvcf MAF_HCMregions.vcf.gz --plink-tped

VCFtools - v0.1.8
(C) Adam Auton 2009

Parameters as interpreted:
	--gzvcf MAF_HCMregions.vcf.gz
	--plink-tped

Using zlib version: 1.2.3
Versions of zlib >= 1.2.4 will be *much* faster when reading zipped VCF files.
VCF index is older than VCF file. Will regenerate.
Building new index file.
	Scanning Chromosome: 1
	Warning - file contains entries with the same position. This is not supported by vcftools, and may cause unexpected behaviour.

	Scanning Chromosome: 2
	Scanning Chromosome: 3
	Scanning Chromosome: 4
	Scanning Chromosome: 6
	Scanning Chromosome: 7
	Scanning Chromosome: 8
	Scanning Chromosome: 10
	Scanning Chromosome: 11
	Scanning Chromosome: 12
	Scanning Chromosome: 14
	Scanning Chromosome: 15
	Scanning Chromosome: 17
	Scanning Chromosome: 18
	Scanning Chromosome: 19
	Scanning Chromosome: 21
Writing Index file.
File contains 5804 entries and 0 individuals.
Applying Required Filters.
After filtering, kept 0 out of 0 Individuals
After filtering, kept 5804 out of a possible 5804 Sites
Error:Require Genotypes in VCF file in order to output as PLINK TPED.
These error messages seem spurious as the vcf's are fine; I have been using them in plinkseq no problem. Any advice?
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