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Old 03-24-2016, 08:16 AM   #1
carolW
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Default extract clinical significant of a vcf variants from clinvar

how can I extract the clinical significant of variants of my vcf file from clinvar? Should I parse the clinvar xml file and match the variants of vcf with those in clinvar if they are annotated similarly or in the same way chr, pos,ref, allele?

Any info is welcome.

Carol
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Old 03-24-2016, 08:35 AM   #2
blancha
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No need to reinvent the wheel, and write your own script.

Just download the ClinVar variants in the VCF format, and use SnpSift Annotate to annotate your own VCF file with the downloaded VCF file.

[Edit]
I did it a long time ago, and I seem to remember having a problem with this method not taking into account the base change, only the coordinates of the mutation, so I ended up having to write my own R script. Since this was a year or two ago, this bug may have been resolved.

Last edited by blancha; 03-24-2016 at 08:38 AM.
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Old 03-25-2016, 12:24 AM   #3
carolW
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can the clinical significance values be used as they are extracted or any other info from the same or other sources such as statistical significance be associated?
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