Last updated: 2019-12-06
Checks: 2 0
Knit directory: PSYMETAB/
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File | Version | Author | Date | Message |
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Rmd | b503ef0 | Sjaarda Jennifer Lynn | 2019-12-06 | add more details to website |
html | 9f1ba5e | Jenny Sjaarda | 2019-12-06 | Build site. |
Rmd | c1d579b | Jenny | 2019-12-04 | add details on data |
provided from iGE3
.strand
file.miss
file.multiple
fileQuery: >The chip used to generate the data was the GSAMD-24v2, however about 10,000 custom SNPs were also added to the chip. Do you have any recommendations for adding such SNPs to the strand file for processing?
Response: >If you have a chip with custom content on it as you do if you are able to send me the .csv annotation file (that contains the TopGenomicSeq information) I can use that to create you a custom strand file that you can then download on a private link, this will ensure the extra SNPs are not lost in the strand update (at the moment they would be removed as non-matching).
Zipped strand files were copied to SGG server (${project_dir}/data/raw/reference_files/) and subsequently unzipped and used in QC (only b37 files was needed).
mv data/raw/phenotype_data/GSA_sex-ethnicity.xlsx data/raw/phenotype_data/QC_sex_eth.xlsx