filter VCF by HGVS - indel normalisation
1
0
Entering edit mode
3.4 years ago

Hi,

I have a list of variants in HGVS notation (c. and p.) and I want to find them in VCF files. I'm looking for the best way to do so.

Since the HGVS notation can vary (e.g. NM_000059:c.1813_1814insA vs. NM_000059:c.1813dup), I thought I'd use the genomic position as a filter.

I tried using VEP to get the genomic position, using HGVSc as input (online tool). But there's a problem with indels in repetitive area, which can be positioned at different locations.

See https://www.ensembl.info/2018/06/22/cool-stuff-the-vep-can-do-normalisation/ :

"The standard way to report an insertion or a deletion in a VCF file is to write it in terms of the base upstream of it. HGVS works differently, they report the position of an insertion or a deletion in a repeat as the last position within the repeat. Since HGVS notation is in terms of the transcript, this means that for negative-stranded transcripts, the reported position is the same as that that would appear in VCF, but for positive-stranded transcripts, a different position is reported."

I need a way to get the position of the indels from HGVS notation, left-aligned as they would appear in a VCF files. Or - go with a different way of filtering... but which?

Can I solve my problem using VEP? and if not, how?

Example:

HGVS to find: NM_000179:c.3984_3987dup (I also have this info: p.Leu1330ValfsTer12)

VEP VCF position: 48033776 (using NM_000179:c.3984_3987dup as input)

My VCF files position: 48033769 (HGVS appears as NM_000179:c.3987_3988insGTCA )

thanks!

Emily_Ensembl

VCF VEP • 1.0k views
ADD COMMENT
0
Entering edit mode

Emily_Ensembl

Perhaps you missed my question..? thanks!

ADD REPLY
1
Entering edit mode
3.4 years ago
Emily 24k

I'm afraid the VEP doesn't have the ability to left-shift to VCF style formatting for repeat expansions/retractions. You could try running your VCF through the VEP getting HGVS notation with 3' shifting then use the HGVS for matching.

ADD COMMENT

Login before adding your answer.

Traffic: 1502 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6