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

Question

[mayara.salvian]

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.

Answer 1

[Pierre Lindenbaum]

there is no genotype in your vcf.

check with

grep CHROM -m1 input.vcf

[mayara.salvian]

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.

[Pierre Lindenbaum]

what was the output of the command please.

[mayara.salvian]

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.

[finswimmer]

Hello mayara.salvian ,

please show us the first lines of the variants.

fin swimmer

[mayara.salvian]

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.

[finswimmer]

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

Answer 2

[2720725749]

i have solve the problem. 我刚刚就遇到了这个问题，并且成功解决了。 当我在比对的时候加上-R参数（bwa mem -M -t 16 -R '@RG\tID:E1\tPL:illumina\tLB:library\tSM:E1' ./ref/ref.fasta ./fqdata/SRR21936710_1.fastq fqdata/SRR21936710_2.fastq > align_bam/E1.sam）,当我进行到vcftools --vcf时，就会出现该错误（vcftools Error: Require Genotypes in VCF file in order to output as 0/1/2 matrix） 然而，如果我将-R参数去除，这时候进行到vcftools --vcf时，就能够成功识别到geno type,完成后面的矩阵转化

[Ram]

Translated using Google Translate:

i have solved the problem. I just encountered this problem and solved it successfully. When I add the -R parameter when comparing (bwa mem -M -t 16 -R '@RG\tID:E1\tPL:illumina\tLB:library\tSM:E1' ./ref/ref.fasta . /fqdata/SRR21936710_1.fastq fqdata/SRR21936710_2.fastq > align_bam/E1.sam), when I proceed to vcftools --vcf, this error will appear (vcftools Error: Require Genotypes in VCF file in order to output as 0/ 1/2 matrix) However, if I remove the -R parameter and proceed to vcftools --vcf, I can successfully identify the geno type and complete the subsequent matrix conversion.