Vcf File Format Qual Column

Question

[User6891]

I'm generating a VCF file which consists of genotype data from 5 individuals. For each variant from each individual I have a Phred Quality Score. But I want to make a VCF file in which I can put the genotypes of these 5 individuals, so what do I have to fill in then in the QUAL column of my .vcf file? Do I have to sum up the 5 individual Phred scores?

[Andreas]

Are you sure that pooling genotypes from several individuals into one vcf-file is valid according to the format? Also, keep in mind that Phred scores are actually probabilities

[User6891]

Normally VCF files can contain genotypes from different individuals for the same position.

Maybe I should give an example of what I want to do: I have a variant file with the following info on each line: Suppose I have a variant on chromosome 1, position 10154262, reference allele = A, alternative allele=G; variant allele frequency+Phred score individual 1; variant allele frequency+Phred score individual 2; variant allele frequency+Phred score individual 3.

Now in a .vcf file you need to fill in for every variant a column named 'QUAL'. But since I have 3 individual Phred Scores, what should I put then in the column QUAL?

Answer 1

[Raony Guimarães]

Use vcf-concat:

vcf-concat A.vcf.gz B.vcf.gz C.vcf.gz | gzip -c > out.vcf.gz

http://vcftools.sourceforge.net/perl_module.html#vcf-concat

[Andreas]

Nice. However, this is for merging different vcf files for one individual (one per chromosome etc). What would happen if you had two variants at the same position in the input files?

Answer 2

[Laura]

If you have no per site score you could use . to represent missing data and supply the per individual score in the individual column along with the genotype