Tool:New VCF Header (schema) Parser---Please Break!!!

Question

[ariel]

I wrote this parser because I couldn't find another utility that did exactly what I want, which is to parse the header and return the schema and metadata in JSON format. In particular, I need a JSON format schema to use when uploading a VCF as a table to BigQuery.

https://github.com/abalter/vcf_header_parser

Currently, the tool does both and includes many options. One To Do item is to facilitate other cloud platforms and database types.

Please stress test!

Answer 1

[d-cameron]

There is now an 'official' VCF test suite. It covers the basics but there are many edge cases (e.g. correct handling of UTF-8 and what to do when the VCF contains invalid UTF-8 encoding) yet to be added to the test suite. You can find it at:

https://github.com/samtools/hts-specs/tree/master/test/vcf