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?
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written
by
bioroma.spb
Yes, I have this spec. I do not understand this particular example described above.
How To Ask Good Questions On Technical And Scientific Forums, Scroll down to the section on explaining to others what you have already done.
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,
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written
by
Ibrahim Tanyalcin
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