Strict VCF Parser
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README.md

README.md

VCFImp

VCFImp is a Scala library for parsing and writing VCF (and VCF-like) files.

Currently, the parser is rather strict. It requires all INFO and FORMAT fields used are previously defined in the VCF's metadata. It'll also validate that the fields values are indeed instances of the type indicated in the metadata and that the correct arity is being adhered to.

vcflatten

This is a command line tool for "flattening" a VCF (4+) file down to simpler TSV files. Essentially, it takes the information from the INFO column and from the sample columns and spreads them out into their own, separate columns.

Check out our documentation page on the web site for more info.

annovcf

This is a command-line tool that automates the merging of ANNOVAR variation annotation into a VCF file. It will put the annotations into the appropriate VCF field (eg. INFO field) and create the necessary metadata at the top of the VCF file.

Check out our documentation page on the web site for more info.

vcfimp-solr

This is a set of classes for importing a VCF file into Solr.

Building VCFImp

If you wish to compile the source yourself, you'll need to get Scala and SBT. After, you can just build the project using sbt. If you make any changes, make sure the tests still pass:

$ sbt
> test

The apps (namely vcflatten right now) have an additional SBT task "dist" that generates a zip file distribution of the app.

$ sbt
> project vcflatten
> dist

This will create a file vcflatten/target/vcflatten-VERSION.zip, which has any additional scripts and documentation in it, along with a JAR file that contains the app, Scala's library, and all other dependencies in it.