Nicole Deflaux

agree

And we should have a dataflow pipeline that goes with it that reads an annotation database from Google Cloud Storage and writes to the [Annotations API](https://cloud.google.com/genomics/v1beta2/reference/annotations/create).

Only 9 warnings remain after https://github.com/googlegenomics/readthedocs/commit/d922f63f45fabf5945155c51bfbc8af9f25eb8dd

There are some newer versions of the [Bioconductor docker containers](https://www.bioconductor.org/help/docker/). In the click-to-deploy user interface, choose "custom" and then enter for example `bioconductor/release_core2`. Let me know if that fixes it...

With `--hasNonVariantSegments` it is performing the same merge as is used in https://github.com/googlegenomics/codelabs/tree/master/Java/PlatinumGenomes-variant-transformation so that it has all the genotypes for each SNP site in the cohort as input to...

@jirkadanek Thanks so much for these detailed instructions!!! We will make it so.

For example compare: ``` SELECT contig, position, reference_bases, GROUP_CONCAT(alternate_bases) WITHIN RECORD AS alt, vt, END, super_population, IF(af >= 0.05, TRUE, FALSE) AS is_common_variant, IF(genotype.first_allele > 0 OR genotype.second_allele > 0,...

agreed, can be simplified I'm pretty sure that pattern is in a few other places too, filed #14 please point out other things like this! Thanks Felipe

@tomasramanauskas sorry for the trouble! We should clarify that some of the queries in this repository are [legacy SQL](https://cloud.google.com/bigquery/docs/reference/legacy-sql) whereas others are [standard SQL](https://cloud.google.com/bigquery/docs/reference/standard-sql/). Here are the instructions to enable...

You are correct - that table is currently unavailable. Here are the details about it: http://googlegenomics.readthedocs.io/en/latest/use_cases/discover_public_data/tute_genomics_public_data.html We have reached out to the owners of the table. Hopefully it will be...