Editing GSCAN (section)

== Internal historical notes ==
Forgive the organization of this page. It has been used historically both as an outward-facing page, but also for internal purposes. Below are items from the past decade of GSCAN. 

*'''Phenotype workgroup:''' Laura Bierut, Marilyn Cornelis, Dave Hinds, Youna Hu, Jaakko Kaprio, Eric Jorgenson, Dajiang Liu, Matt McGue, Marcus Munafo, Gunter Schumann, Scott Vrieze, Luisa Zuccolo
*'''Analysis workgroup:''' Goncalo Abecasis, David Hinds, Youna Hu, Eric Jorgenson, Charles Kooperberg, Pete Kraft, Penelope Lind, Dajiang Liu, Nancy Saccone, Dan Stram, Scott Vrieze, Xiaowei Zhan

=== Phenotype definitions and analysis plan ===
The analysis plan and phenotypes are described in files linked below (makes it easier to keep track of versioning!). Coding of phenotypes is described in the aptly-named "phenotype definitions" file whereas the genome-wide analysis plan is in the all-too-aptly-named "analysis plan" document. Please note that the phenotype definitions document only contains information on how to code the eight smoking/drinking phenotypes. File formats for those phenotypes, which many will recognize as standard pedigree formats, are included in the analysis plan. Everything else should be fairly straightforward.

[[Media:GSCAN_GWAS_ANALYSIS_PLAN-v1.4.docx | Click here to find the GSCAN GWAS analysis plan.]]

[[Media:GSCAN_GWAS_Phenotype_Definitions-2-24-2016.pdf | Click here to find the GSCAN GWAS phenotype definitions.]]

=== Coordination and organization ===
Progress, internal and external, are tracked in [https://docs.google.com/document/d/1kWaY40n-bSURoLW7VcU9CFv08zVx360RHmxvL7DIreU/edit '''this Google Doc''']. More specific progress on internal studies is  [https://docs.google.com/spreadsheets/d/1canvCaAJW70LjSHidtvwrJgyDMa_ZlT7dvpzOsz6PNY/edit#gid=0 '''tracked here'''].

Study contact info is tracked in [https://docs.google.com/spreadsheets/d/11apZaSyesNy4hl4MIgrKRYSASrwZM2iEJsuuFQByCfI/edit#gid=0 '''this Google Sheet'''].

Studies available in dbGaP, along with accession numbers, etc. are tracked in [https://airtable.com/tblzZUtQWcZSlfjrA/viwhISDznphLfST8m '''this Airtable'''].

===File locations===
Study data to which we have direct access are located either on twins or RC. Twins data are organized in the folder /net/twins/svrieze/everything-else/wp/GSCAN/GWAS. Within this folder those studies to which we have raw data access are in the folder ''CU_Boulder_samples'' (for lack of a better name!). Summary stats generated on these samples are organized within ''summary_stats_generated_internally''. Summary stats generated by outside groups and submitted for meta-analysis are organized within ''summary_stats_generated_externally''.

On RC the organization is similar. Everything is located within the folder /work/KellerLab/GSCAN/GWAS. Study data to which we have raw data access are in the folder ''individual_level_study_data''. Summary stats generated on these samples are organized within ''summary_stats_generated_internally''. Summary stats generated by outside groups and submitted for meta-analysis are organized within ''summary_stats_generated_externally''.

===[[GSCAN dbGaP]] & UK Biobank===
Studies included from dbGaP, and the process by which phenotypes and genotypes were constructed and merged is outlined on the [[GSCAN dbGaP]] page.

===Meetings===
Regular conference calls are held and minutes are [https://docs.google.com/document/d/1ZK9VIXxcej3lat_oD_oxPP0ajHwj8yX_FKaPh53svVo/edit# '''available here'''.]

Other meeting materials from internal meetings are here:

[[GSCAN 6/16/16 -- dbGaP & GfG]]