VCF2MAF and allele frequency

[jmf432x]

VCF2MAF and allele frequency

[jmf432x]

anyone?

[tanghaibao]

In my VCF, the AF field is in the FORMAT column, so I could get VAF with --retain-fmt AF instead of --retain-info.
Then the VAF column is t_AF in the resulting MAF.

[berguner]

@tanghaibao AF in the FORMAT column represents the allelic fraction which is the fraction of reads supporting the variant in that sample. @jmf432x is asking about population allele frequency of the variant seen in the population databases like GnomAD or dbSNP.

Back to the original issue, I am also missing GnomAD AF in my MAF file. Would be interested if anyone has figured out the issue and a solution.

[grantn5]

Hi @berguner I have been using the

Nextflow pipeline here (dev branch)

https://github.com/FriederikeHanssen/vcftomaf/tree/dev

To do the conversion it automatically includes all VEP annotations present in the info column