HGVS to VCF conversion

Question

[luisantome]

hi everyone,

I have a very large data set of genomic variants in hgvs format and I want to convert it into vcf format.

I've tried ensembl VEP tool. It works great for SNVs but in indels I need to get the Ref/Alt alleles because the next tool I use doesn't deal with N's

Input example:

NM_000059.3:c.8332-1603delT

VEP output:

#CHROM    POS    ID    REF    ALT
13    32368798    NM_000059.3:c.8332-1603delT    NT    N

Desired output:

#CHROM    POS    ID    REF    ALT
13    32368798    NM_000059.3:c.8332-1603delT    GT    G

Please let me know if there is any tool which allows this conversion or provide me some guidance to do it manually by scripting.

Thank you in advance

[luisantome]

thank you guys for your kind replies!

I also found the hgvs library googling the internet.

I'll give it a chance. Wish me luck!

Thanks again!

Answer 1

[hns]

There is a python library that does that. You can check that out. It is very straight forward to use and install.

https://github.com/counsyl/hgvs

Answer 2

[EnsemblWill]

VEP will add the preceding bases to indels if you use the --database flag (in place of --cache which I assume you are currently using).

If you update your VEP installation (re-run the INSTALL.pl script to grab the latest API code), then it should now also work with --cache. Performance will also be improved if you have a FASTA file set up for sequence retrieval (the INSTALL.pl script can fetch this for you, or see http://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#fasta)

[luisantome]

thanks for sharing! so far I've used VEP via web interface but now I'm encouraged to install the API and test it in depth

Answer 3

[Jeremy Leipzig]

Seems like you just need reference bases?

http://genome.ucsc.edu/cgi-bin/das/hg19/dna?segment=chr13:32368798,32368798