Manual annotation of complex indel in VCF

Question

[bioroma.spb]

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?

Answer 1

[Emily]

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

[bioroma.spb]

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

[Emily]

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

Answer 2

[Ibrahim Tanyalcin]

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,