Matching my VCF genome with ClinVar
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10 weeks ago
vpsev3 ▴ 10

Hello,

I'm desperately trying to match my genome with ClinVar, I've been on it for several hours but nothing is working

Now I have found this software which looks good https://github.com/brentp/slivar

But I don't understand anything about the parameters, I have my genome in vcf.gz and the ClinVar database in the same format aligned with the GRCh38, I would like to find variants referenced as "pathogenic" or "likely pathogenic"

Can you help me ?

Thank you.

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Have you tried using a simple bcftools annotate? You should also vt decompose and vt norm before using bcftools to ensure your VCF is left-aligned and decomposed to only bi-allelic entries.

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Are you doing this for your own genome? Have you thought about what you will do if you have variants defined as 'highly pathogenic'? Interpreting these things is hard and you should only really trust the results when performed and interpreted by experts. (Sorry if you're an expert - I've just come across people who try and self-diagnose and end up getting very anxious about the results they get).

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Yes I'm ready to have these kind of results, if I find any I will read the studies and see, but there are a lot of things wrongly labeled as pathogenic on ClinVar

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Try ANNOVAR command line version:https://annovar.openbioinformatics.org/en/latest/user-guide/startup/.

If you have variant file then convert it to annovar input. Then you need to download latest Clinvar data using function (annotate_variation.pl) and then run table_annovar.pl with Clinvar_version.

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