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.
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written
by
mayara.salvian •
there is no genotype in your vcf.
check with
grep CHROM -m1 input.vcf
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.
what was the output of the command please.
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.
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.
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
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
Translated using Google Translate:
I have solved the problem. I just encountered this problem and solved it successfully. When I add the
-Rparameter 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 tovcftools --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-Rparameter and proceed tovcftools --vcf, I can successfully identify the genotype and complete the subsequent matrix conversion.
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.
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