This package was created to extract the variants from a VCF file, annotate them with data from the ExAC API, and export an easy to read table for investigators, as well as a re-annotated VCF for downstream analyses.
I tried to limit the dependencies, but didn't want to reinvent the wheel. This
package requires VariantAnnotation
and dplyr
as R dependencies, and needs
jq
and curl
to be installed on the system (these are in the Debian and Ubuntu Repos).
VariantAnnotation
has a lot of dependencies, one of which (XML
) required the
installation of libxml2-dev
on my system.
scripts/vai.R
provides all the code needed to generate out/table.csv
which
contains a simple table of relevant info for all variants (for the
investigator), as well as out/vai_exac_annotated.vcf
which is an annotated VCF
file for use in other analyses which might need a VCF.
The exec/exac_lookup.sh
script can also be used as a standalone tool to
perform single queries of ExAC.
I packaged the input VCF file in inst/extdata
so that it can be called by the
script portably. I also put the output table and VCF in out
.
I recommend installing with devtools::install_github('ahopki14/vai')
. Then
vai.R
can be run and should have everything it needs.
table.csv
?Header | Description --------------|------------ Type | Type of variant, i.e. snp, ins, etc. AlleleFreq | Allele Frequency reported in the VCF ReadDepth | Total reads covering the variant GenoType | 0/1,0/2, etc.=Heterozygous, 1/1=Homozygous AltReads | Number of reads supporting the Alternate RefReads | Number of reads supporting the Reference PctAlt | Percentage of reads supporting Alternate VariantNames | chr-pos-ref-alt, Used to query the ExAC database Consequence | The reported Major Consequence from ExAC PopAlleleFreq | The frequency of the variant in the ExAC data PolyPhen | Score summarizing the impact of the mutation (0=benign, 1=major) GeneName | If the variant is in ExAC, the gene SYMBOL of the gene containing the variant
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