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how to change indel to smallest length in vcf

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.

next-gen annotation indel vcf
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written by kumajis • kumajis

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

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written by finswimmer finswimmer

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