Question: how to change indel to smallest length in vcf
gravatar for 1097049297
18 months ago by
10970492970 wrote:

I want to annotate VCF with HGMD database information by sql, but there is some problem with indel records, such as :

In VCF the variant is 5 13868103 . TA T, but in HGMD, it becomes 5 13868104 A .

So for annotation correct, should I change variants like 5 13868103 . TA T to 5 13868104 . A . in VCF (if so, what tools could do this), or there are some other ways to solve it.


vcf next-gen annotation indel • 346 views
ADD COMMENTlink written 18 months ago by 10970492970

Hello 1097049297 ,

if possible you should try to make a vcf out of the sql database and normalize the result with bcftools norm.

fin swimmer

ADD REPLYlink written 18 months ago by finswimmer13k
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