Updated bigquery-examples content for 1,000 genomes to current variants schema

[deflaux]

Changes included

1. first_allele, second_allele fields are now repeated field genotype (this necessitated many changes to the structure of queries)
2. table name change and many column name changes
3. data has been changed from 1-based genomic coordinates to 0-based coordiantes
4. sample_info and pedigree tables we re-created from the source
   1. which included a super population name change from ASN to EAS
   2. provenance details include instructions to pull from source and load directly into BigQuery
5. annotation tables moved into their own dataset
6. updates to bigrquery usage
7. refactoring of content such that getting started material and the literate programming demo have been moved to new repository getting-started-bigquery

[cassiedoll]

nice cleanup! I made just a couple of comments. Definitely merge whenever you are ready.

[pgrosu]

Hi Nicole and Craig,

Overall it looks really nice, and you guys have done an amazing job! So out of curiosity, I randomly picked and ran the following query via the browser:

SELECT type, count(1) cnt FROM [google.com:biggene:annotations.clinvar] group by type

I noticed as a result that I got the following error - I obfusicated my project ID:

Query Failed
Error: Access Denied: Table google.com:biggene:annotations.clinvar: QUERY_TABLE
Job ID: ...:...

I took this query from the following page:

https://github.com/deflaux/bigquery-examples/blob/master/1000genomes/data-stories/annotation-joins/README.md

It might be best to have someone from the outside test all the queries and run all the programs, in order to ensure that the experience is the same in terms of results and maybe performance.

Just a recommendation, Paul

[deflaux]

@pgrosu thanks for pointing that out! Permissions have been fixed.

[pgrosu]

No problem, glad to help Nicole :)