Vcf File Format Qual Column
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8.9 years ago
User6891 ▴ 290

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?

vcf quality • 4.3k views
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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

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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?

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8.9 years ago

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

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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?

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8.9 years ago
Laura ★ 1.7k

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

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