Gff To Vcf

Question

[win]

Hi there, I was wondering if someone could help.

Can a GFF file be converted to a VCF?

If so can someone please point me in the right direction.

Thanks, A

Answer 1

[Michael]

In general it is not possible to convert the data in a GFF file to VCF format without loss of information. This is because of the different scope of the format. GFF is mostly used to contain genomic features (aka. genome annotations), e.g. genes, transcripts, exons and their relations. It does not encompass concepts like alleles, allele frequencies, and samples or populations. On the other hand, VCF does not contain anything but concepts related to variants (SNPs, CNVs). Trying to convert general GFF to VCF would be abuse of the format, except for the single case that GFF contains solely locations of variants (e.g. a SNP track downloaded from a genome browser) . The allele information would then either be lost or must be encoded in some awkward tags in the GFF.

tl;dr most likely not, but please provide an example.