Nicole Deflaux

The integration tests currently take 32 minutes to complete. Of that: - 8 minutes for the tests that run locally on tiny data - 24 minutes for the tests that...

When https://github.com/googlegenomics/api-client-java/issues/66 is complete, add a check to VerifyBamId to WARN with a yes/no to proceed if the referenceSets for the reads and the variants do not match.

This repository is bloated due to checking in a few bundled jars, fixed via https://github.com/googlegenomics/dataflow-java/issues/49 Let's scrub out those obsolete jars via https://help.github.com/articles/remove-sensitive-data/ to reduce the bloat.

Per https://cloud.google.com/bigquery/user-defined-functions

There appears to be a bug in https://github.com/googlegenomics/bigquery-examples/blob/master/pgp/sql/gvcf_variants/allele-count.sql Specifically its not incrementing the alternate_allele_count when genotype 2 corresponds to the allele in question. Here's our result: ``` SELECT contig_name, start_pos,...

Since "the same" variant can occur on multiple records in our tables (see example records shown by query below), it breaks the experiment we are trying to do with table...

for an example see #13

optimize all queries using FLATTEN

3

Restructure them so that the clause within the FLATTEN returns only the columns needed and also applies any applicable WHERE clauses.

on README.md