Basic Shiny app to fetch variant information

I created a basic Shiny app that uses the myvariant package to fetch variant information from MyVariant.info. The variants need to be represented in the format recommended by the Human Genome Variation Society. Once you have your variant of interest in the correct format, just hit "Get variant info!" and the annotations will appear on the right. You can find the app hosted at: https://davetang.shinyapps.io/get_variant_info/.

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Web traffic to date

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I'm going to include my blog as a form of community engagement in my fellowship application. The only objective way I can measure its impact is by the number of views. Luckily the WordPress API makes it easy to download all my web traffic and I have made this data available online. I wrote this post in case one of the assessors decided to check whether I was just making up numbers.

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ExAC allele frequency of pathogenic ClinVar variants

A continuation of the post on the genomic location of pathogenic ClinVar variants. For this post I will use vcfanno to annotate the ClinVar variants with the ExAC VCF file.

To get started, download the ExAC VCF file.

# 4.1G file
wget -c ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz
wget -c ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/ExAC.r0.3.1.sites.vep.vcf.gz.tbi

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Sporadic WordPress 500 Internal Server Errors

I finally found the reason behind the sporadic 500 internal server errors on my blog. It was caused by the iThemes Security plugin, which had modified the .htaccess file in a manner that was causing the errors. I have disabled the plugin and the site seems to be running fine now. I've also added HTTPS on my domain, so you can now access my blog on https://davetang.org/muse/. Enjoy!

Genomic location of pathogenic ClinVar variants

How many pathogenic ClinVar variants are in intergenic regions? I'll define genomic regions as per this old post. To get started, download the latest ClinVar variants:

wget -c ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar_20170104.vcf.gz

# index
tabix -p vcf clinvar_20170104.vcf.gz

# how many variants?
zcat clinvar_20170104.vcf.gz | grep -v "^#" | wc -l
232624

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