Question
Question Posted 06/26/13:
Hi Genetic Core experts, I have a two-folded question. 1) Are the .csv files annotated raw files from Illumina? How do you match the SNP name with dbSNP id's?
2) Was the plink file generated using these .csv files? What was the workflow?
Thank you.
Hi Genetic Core experts, I have a two-folded question. 1) Are the .csv files annotated raw files from Illumina? How do you match the SNP name with dbSNP id's?
2) Was the plink file generated using these .csv files? What was the workflow?
Thank you.
Response posted 06/26/13 by Andy Saykin:
1) The .csv files (Final Report Files) contain the SNP information present in Illumina's manifest file. This file along with other Illumina files and intensity data files were analyzed in GenomeStudio (Illumina software) to produce the Final Report files posted to LONI. More information on SNPs of interest is available by searching the refSNP ID on dbSNP (http://www.ncbi.nlm.nih.gov/projects/SNP/).
2) The PLINK files were generated from the GenomeStudio project file. The correct ADNI IDs were added in the Final Report files and PLINK files so these are the formats released.
2) The PLINK files were generated from the GenomeStudio project file. The correct ADNI IDs were added in the Final Report files and PLINK files so these are the formats released.
