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Arc39 / vcf_to_ga

converts VCF into GA4GH protobuf messages
Apache License 2.0
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Attribute matching #15

Open david4096 opened 8 years ago

david4096 commented 8 years ago

Write a function that runs against the mongodb to return variants with key/value pair matches.

Write a function that returns variants with allele frequency over some threshold.

Identify all patients with variants annotated as pathogenic in clinvar identify all patients with a rare (MAF<1%) variant predicted to be pathogenic by SIFT or PolyPhen or CADD score.

david4096 commented 8 years ago

I'm working on a new calls search pattern and your code is a great place to test out the queries. https://github.com/ga4gh/schemas/pull/655

david4096 commented 8 years ago

This could be a separate notebook against the DB. Check out matplotlib.