Vcftools --Freq

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11.5 years ago

kai.clarkson ▴ 30

I'm getting some really confusing results using vcftools and I was wondering if anyone could shed some light. I have merged 5 individual SNP call .vcf files using vcf-merge. This merged file seems fine until I try to calculate allele frequency from it (--freq). Some of the allele freq are correct (compared to calculating by hand) but some are wrong. The Fst calculator (--fst-pop) also throws up some weird highly negative scores.

The genotype scores for the individuals all seem to be correct (the same as the source files) in the rows that give wrong allele frequencies, so how is vcftools getting an incorrect value?

Any help would be greatly appreciated,

Regards,

Kai

vcftools allele frequency vcf • 5.9k views

ADD COMMENT • link 11.5 years ago by kai.clarkson ▴ 30

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I have never worked with calculating AF from a merged vcf file using --freq option.What I have noticed is the merged file you get from vcftools usually takes AF from the first vcf input.It doesn't give you an average of the AF over all the samples.I am not sure if this would help,but just an idea.