Question: vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.
0
gravatar for mayara.salvian
4 days ago by
mayara.salvian10 wrote:

Hi everyone,

I have a vcf-file and I'm trying to convert my vcf file into 012 genotype matrix using the following code:

vcftools --vcf myfile.vcf --012 --out out_file

I didn't have problems when I run this code before, however now the following error message appears:

Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix.

I've tried increasing the number of temporary files allowed by the operating system used (e.g. ulimit -n 1000), but still didn't work.

Could someone help me? Thanks.

vcftools vcf • 125 views
ADD COMMENTlink modified 4 days ago by Pierre Lindenbaum112k • written 4 days ago by mayara.salvian10
0
gravatar for Pierre Lindenbaum
4 days ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

there is no genotype in your vcf.

check with

grep CHROM -m1 input.vcf
ADD COMMENTlink modified 4 days ago • written 4 days ago by Pierre Lindenbaum112k

Yes, according with the error message there is no genotype in my vcf. However I checked my file using your suggestion and there is genotype on it.

ADD REPLYlink written 4 days ago by mayara.salvian10

what was the output of the command please.

ADD REPLYlink written 4 days ago by Pierre Lindenbaum112k
1

The output of the command showed me only the following columns: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ID1 ID2 ID3 ... IDn Where: ID1, ID2, ID3 until IDn are the samples' ID.

ADD REPLYlink written 4 days ago by mayara.salvian10

Hello mayara.salvian ,

please show us the first lines of the variants.

fin swimmer

ADD REPLYlink written 4 days ago by finswimmer6.1k

Hello finswimmer,

These are the first seven lines of my file:

#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ID1* ID2* ID3* ID4* ID5*
chr1 POS1 ID1 A G . . . GT 0/0 0/1 0/0 0/0 0/1     
chr1 POS2 ID2 T C . . . GT 0/1 0/1 0/0 0/0 0/0     
chr1 POS3 ID3 G A . . . GT 0/0 0/1 0/1 0/0 0/1     
chr1 POS4 ID4 G C . . . GT 0/1 0/0 0/1 0/0 0/1     
chr1 POS5 ID5 A G . . . GT 0/1 0/0 0/0 1/1 1/1     
chr1 POS6 ID6 A G . . . GT 0/0 0/1 0/1 0/0 0/1

Where: ID (1..6) are the SNPs' ID and ID*(1..5) are the Samples' ID.

ADD REPLYlink modified 4 days ago • written 4 days ago by mayara.salvian10

Hello again,

just a guess: Maybe the * in the sample names makes some problems here. Remove them from the names and try again.

fin swimmer

ADD REPLYlink written 1 day ago by finswimmer6.1k
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