Last updated: 2019-12-06

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Knit directory: PSYMETAB/

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Rmd b503ef0 Sjaarda Jennifer Lynn 2019-12-06 add more details to website
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Data

provided from iGE3

General information

  • Files received from: Mylene Docquier (Mylene.Docquier@unige.ch), iGE3 Genomics Platform Manager, University of Geneva
  • ftp server details:
  • Genotype data received in genomestudio format on August 28, 2019; for processing and converting to PLINK format see docs/miscellaneous/data_processing.md

Genotype data

  • Genotype data found in data/raw/genotypes
  • Each folder contains:
    • Initial data provided from Mylene in genomestudio format, with the original folder name (‘XXX/’).
    • Cluster files in genomestudio format (see docs/miscellaneous/data_processing.md), and named ‘XXX_cluster/’.
    • PLINK files exported from genomestudio.

Miscellaneous GSA information provided in the following files:

  1. GSA v2 + MD Consortium.csv
  2. GSAMD-24v2-0_20024620_A1.csv
  3. GSAMD-24v2-0_A1-ACMG-GeneAnnotation.xlsx
  4. GSAMD-24v2-0_A1-ADME-CPIC-GeneAnnotation.xlsx
  5. GSAMD-24v2-0_A1-HLA-GeneAnnotation.xlsx
  6. GSAMD-24v2-0_A1-TruSight-GeneAnnotation.xlsx
  7. GSAv2_MDConsortium.bpm
  8. GSPMA24v1_0-A_4349HNR_Samples.egt

Details

  • Files 1 and 2 appear to be identical and correspond to strand illumina strand information, same file can be found here.
  • xlsx files contain 2 tabs: “Coverage Summary” and “GSAMD-24v2-0_A1-XXX-GeneAnnota”
  • bpm file corresponds to manifest file for use in genomestudio. Manifest files provide a description of the SNP or probe content on a standard BeadChip or in an assay product.
  • egt file corresponds to cluster file for making genotype calls.
  • all saved in data/reference_files

Chip details from Illumina

  • Files received from: Fe Magbanua (techsupport@illumina.com),Technical Applications Scientist, Technical Support, Illumina
  • GSAMD-24v2-0_20024620_A4_StrandReport_FDT.txt: strand report build38 (build37 not available).
  • GSAMD-24v2-0_20024620_A1_b151_rsids.txt: loci to rsid conversion file build37.
  • GSAMD-24v2-0_20024620_A4_b151_rsids.txt: loci to rsid conversion file build38.
  • all saved in data/reference_files (copied using FileZilla)

Strand files from Welcome Centre

  • The data for each chip and genome build combination are freely downloadable from the links localted here, each zip file contains three files, these are:
    • .strand file
    • .miss file
    • .multiple file
  • More details can be found at the link above
  • Chipendium was used to comfirm that bim files are on the TOP strand .
  • Contacted William Rayner (wrayner@well.ox.ac.uk) to find out what to do about custom SNPs, all correspondence on 22/07/2019.

    • Query: >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).

    • Trying to obtain such .csv file from Mylene or Smita at Illumina (spathak@illumina.com) who designed the chip.
    • On 15/07/2019 Smita provided such a file: GSA_UPPC_20023490X357589_A1_custom_only.csv.
    • The file was downloaded and save to UPPC (Jenny/PSYMETAB_GWAS/GSA).
    • Sent .csv file to William Rayner and he provided the strand file for the custom SNP list on 16/07/2019:
      • GSA_UPPC_20023490X357589_A1_custom_only-b37-strand.zip
      • GSA_UPPC_20023490X357589_A1_custom_only-b37-strand.zip

    • 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).

Phenotype data

  • Sex and ethnicity data provided by Celine (via email) for each batch on July 18, 2019: GSA_sex-ethnicity.xlsx
  • Downloaded and saved to UPPC folder (Jenny/PSYMETAB_GWAS/).
  • Opened, manually changed all accents to standard letters (ctrl-F and replace) and re-saved as csv/xlsx file (with ‘no_accents’) for easier use in R.
  • Moved to SGG folders via filezilla (manually).
  • Name was changed (see ‘Master.sh’), as follows:
mv data/raw/phenotype_data/GSA_sex-ethnicity.xlsx data/raw/phenotype_data/QC_sex_eth.xlsx