Question: Manual annotation of complex indel in VCF
1
gravatar for bioroma.spb
3.3 years ago by
bioroma.spb50
Saint-Petersburg, Russian Empire
bioroma.spb50 wrote:

Hi, everyone!

I've encountered complex variant of FMR1. It consist of both 157 bp deletion and 7 bp insertion at the same site. What is the correct way to make its VCF notation? This is how I imagine possible notation (simplified):

POS REF ALT INFO
<del 5'> C CACGGAGT SVTYPE=CNV;END=<del 3'>;SVLEN=-157;

I know this variant is far too small for CNV, but just I can't put DEL or INS either. Do you have any ideas how to write it clearly?

variant annotation vcf • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Emily_Ensembl18k • written 3.3 years ago by bioroma.spb50
2
gravatar for Emily_Ensembl
3.3 years ago by
Emily_Ensembl18k
EMBL-EBI
Emily_Ensembl18k wrote:

VCF spec is defined here. Complex rearrangements appear on page 12.

ADD COMMENTlink written 3.3 years ago by Emily_Ensembl18k

Yes, I have this spec. I do not understand this particular example described above.

ADD REPLYlink written 3.3 years ago by bioroma.spb50

How To Ask Good Questions On Technical And Scientific Forums, Scroll down to the section on explaining to others what you have already done.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Emily_Ensembl18k
0
gravatar for Ibrahim Tanyalcin
3.3 years ago by
Belgium
Ibrahim Tanyalcin930 wrote:

Dear,

Whenever I am in doubt of naming variants I consult human genome variation society page: http://www.hgvs.org/mutnomen/

However in your case if you want to form a machine readable format, I would suggest you just simplify the 157bp ins and 7bp del to form a single insertion and write it your REF and ALT columns in your tsv file. the Info column can further be elaborated.

Hope this helps,

Regards,

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Ibrahim Tanyalcin930
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1034 users visited in the last hour