Question

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

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6.1 years ago

mayara.salvian ▴ 10

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 • 7.7k views

ADD COMMENT • link updated 12 weeks ago by Ram 44k • written 6.1 years ago by mayara.salvian ▴ 10

score 0 · Answer 1 · 2018-10-11

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6.1 years ago

Pierre Lindenbaum 164k

there is no genotype in your vcf.

check with

grep CHROM -m1 input.vcf

ADD COMMENT • link 6.1 years ago by Pierre Lindenbaum 164k

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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 REPLY • link 6.1 years ago by mayara.salvian ▴ 10

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what was the output of the command please.

ADD REPLY • link 6.1 years ago by Pierre Lindenbaum 164k

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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 REPLY • link 6.1 years ago by mayara.salvian ▴ 10

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Hello mayara.salvian ,

please show us the first lines of the variants.

fin swimmer

ADD REPLY • link 6.1 years ago by finswimmer 16k

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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 REPLY • link 6.1 years ago by mayara.salvian ▴ 10

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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 REPLY • link 6.1 years ago by finswimmer 16k

score 0 · Answer 2 · 2022-10-23

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2.0 years ago

2720725749 • 0

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

ADD COMMENT • link 2.0 years ago by 2720725749 • 0

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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 genotype and complete the subsequent matrix conversion.

ADD REPLY • link 12 weeks ago by Ram 44k

score 0 · Answer 3 · 2024-08-05

I'm late to the party, but I was able to fix this issue by replacing the spaces between column names in the header line (beginning with #CHROM) with tabs. The hint was that vcftools was telling me that it expected #CHROM to be the "First Header entry", but the First Header entry was a list of every single column name, including all my sample names. It was treating the whole line as a single header string, as there were no tabs to delimit the columns. I used a simple find-and-replace in Notepad++ to manually replace the spaces with tabs, and was able to perform my desired analyses with vcftools afterward.

For what it's worth, I also removed unusual characters from my sample names before this (in my case, "/"). I'm unsure if that was also necessary.