uk_biobank:downloading_the_data
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uk_biobank:downloading_the_data [2016/02/29 11:22] scott /* Phenotypic data */ |
uk_biobank:downloading_the_data [2016/03/15 12:09] luke /* Quality Control */ |
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| - Genetic data is downloaded following the instructions at [[http:// | - Genetic data is downloaded following the instructions at [[http:// | ||
| - Scripted downloads of all chromosomes were done using a command such as | - Scripted downloads of all chromosomes were done using a command such as | ||
| - | < | + | |
| $ seq 1 26 | parallel -j1 ./gfetch cal {} | $ seq 1 26 | parallel -j1 ./gfetch cal {} | ||
| $ seq 1 26 | parallel -j1 ./gfetch imp {} | $ seq 1 26 | parallel -j1 ./gfetch imp {} | ||
| - | </ | + | |
| - A single sample map (impv1.sample) for the imputed data also was downloaded | - A single sample map (impv1.sample) for the imputed data also was downloaded | ||
| - | < | + | |
| $ ./gfetch imp 1 -m | $ ./gfetch imp 1 -m | ||
| - | </ | ||
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| + | ====== Quality Control ====== | ||
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| + | We identified lists of individuals and positions to exclude from information in the UKB data and in the Axiom Array unimputed genotypes. | ||
| + | - All files can be found on RC at: / | ||
| + | - 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 / | ||
| + | - Additional Affymetrix and UKB information can be found on their websites: | ||
| + | [[http:// | ||
| + | - 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. | ||
uk_biobank/downloading_the_data.txt ยท Last modified: 2020/04/22 11:35 by luev6784
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