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-   -   extract clinical significant of a vcf variants from clinvar (http://seqanswers.com/forums/showthread.php?t=67125)

carolW 03-24-2016 08:16 AM

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

blancha 03-24-2016 08:35 AM

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.

carolW 03-25-2016 12:24 AM

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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