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How can I calculate the variant allelic fraction from the VEP file for multiple human samples?

I used the ensembl-vep and it is human data.

  • 1
    $\begingroup$ Please show a) your VEP output and b) describe what variant allelic fraction means. Thank you. $\endgroup$
    – user438383
    Jun 6 at 14:58

1 Answer 1


If you just have a VEP output (i.e. VCF) without raw genotypes then you cannot calculate the allelic fraction.

  • $\begingroup$ thanks user438383, how can calculate it if i have the vcf file? $\endgroup$
    – Joman
    Jun 6 at 15:29
  • 2
    $\begingroup$ @Joman See: biostars.org/p/147443 $\endgroup$
    – Ram RS
    Jun 6 at 16:04

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