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--- uk_biobank:downloading_the_data [2016/02/29 18:22] – /* Phenotypic data */ scott
+++ uk_biobank:downloading_the_data [2020/04/22 17:35] (current) – luev6784
@@ Line 35: / Line 35: @@
   -  Genetic data is downloaded following the instructions at [[http://biobank.ctsu.ox.ac.uk/showcase/exinfo.cgi?src=AccessingGeneticData|the UK Biobank site]].
   -  Scripted downloads of all chromosomes were done using a command such as
-<code>
 $ seq 1 26 | parallel -j1 ./gfetch cal {}
 $ seq 1 26 | parallel -j1 ./gfetch imp {}
-</code>
   -  A single sample map (impv1.sample) for the imputed data also was downloaded
-<code>
 $ ./gfetch imp 1 -m
-</code>
+====== Quality Control ======
+We identified lists of individuals and positions to exclude from information in the UKB data and in the Axiom Array unimputed genotypes.
+  - A very brief overveiw of QC steps can be found in this .pptx file{{ :uk_biobank:2020_04_22_ukb_qc.pptx |}}.
+  -  All files can be found on RC at: /work/KellerLab/UKBiobank/genetics/raw/Quality_Control
+  -  UKB and Affymetrix performed a number of QC analyses to exclude questionable positions and identify individual samples. Additional pdfs from the UKBiobank are found within /work/KellerLab/UKBiobank/genetics/raw/Quality_Control/UK_Biobank_Axiom_Array
+  -  Additional Affymetrix and UKB information can be found on their websites:
+        [[http://www.ukbiobank.ac.uk/scientists-3/uk-biobank-axiom-array/|UK Biobank Axiom Array]], [[https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=UKB-GENETICS|UKB-Genetics Archive]]
+  -  A list of 1068 individuals to exclude is in Exclude_individuals.poorQC.UKB_Affy_sex.id on RC.
+  -  A list of 8010 positions to exclude is in duplicate.positions.excludesnps.txt on RC.
+  -  A README.txt file located on RC contains the steps used and additional information.