Question: how to change indel to smallest length in vcf
0
gravatar for 1097049297
8 months ago by
10970492970
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.

Thanks.

vcf next-gen annotation indel • 222 views
ADD COMMENTlink written 8 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 8 months ago by finswimmer12k
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: 1483 users visited in the last hour