Human Genome Variant Society format converter

[mehul...@gmail.com]

So I have been exploring this project for few days now in order to write a proposal describing my approach and I have a few concerns.

My first thought about converting a file format to another was that I would gain better insight on this if I can find a same genome file in all 3 formats. Searching on google with the following didn’t get me anywhere.

-> ".hgvs"

-> filetype:hgvs

I am struggling to find even one such trio, if you can help me with this that’d be great.

So my most prior hurdle is that I am finding the terms in hgvs format (http://varnomen.hgvs.org) incomparable to VCF or MAF format for the following reasons :

-Most of the terms used in hgvs specification are not present at all in the VCF format specification pdf. (eg : frame shift, protein, nucleotide)

-Most of the links on this page (https://software.broadinstitute.org/software/igv/MutationAnnotationFormat) that should have helped to understand   MAF format’s specification lead to a https://auth.nih.gov/iTrustGateway which requires authentication.

[Ino de Bruijn]

Hi Mehul,

Thanks for reaching out!

There is no filetype HGVS. Only MAF and VCF.

The HGVS format is a way to represent variants in a single string without spaces. MAF and VCF are both tab delimited formats.

In MAF the format to represent a variant is like this:

https://github.com/genome-nexus/genome-nexus-annotation-pipeline/blob/master/test/data/minimal_example.in.txt

For VCF it is:

https://github.com/inodb/sufam/blob/master/example/sufam.vcf

HGVS is e.g.:

17:g.41242962_41242963insGA

So a column in VCF or MAF could actually contain the HGVSg notation

Hope that clarifies things!

Best wishes,

Ino