Hi all using Illumnia GenomeStudio 2.0.2 software, specifically the Genotyping 2.0.2 module, I have independently processed data from three different SNP arrays:
- HumanOmniExpress-24v1.1
- HumanOmniExpress-24v1.2
- GSA arrays
Using the PLINK Input Report Plug-in v2.1.4 for GenomeStudio Genotyping module I have generated output files from my SNP array data -> .bat, .map, .ped, .phenotype, and .script files
The .map file is of concern here, it contains:
Column 1 -> Chromosome Column 2 -> SNP name Column 3 -> Genetic distance (in cM) Column 4 -> Physical position of SNP (according to hg19, as this is the manifest file that I have used when loading my GenomeStudio project).
The problem that I have encountered:
Regardless of the SNP array being used, there is a section of markers for each chromosome where cM positions suddenly start decreasing in value incorrectly. As far as I can tell, the CM values should only increase or stay the same (ie if two SNPs are in close proximity) when sorted by the physical position of the SNP.
-> This has occurred in output files from independent projects of different array types.
-> I have tried outputting the data again on another occasion with the same issue occurring.
-> I have output files exactly like these from a HumanOmniExpress-24v1.1 chip that were outputted using a plink plugin with the previous version of GenomeStudio and this issue not be evident. Is there a problem with Illumina's Plink plugin?
Has anyone using the Illumina GSA arrays in particular encountered this? or found any clever ways around it? Thanks in advance.
J.
Just in case anyone is following this, I think I have a basic solution... I was able to use the GSA Physical and Genetic Coordinates .txt file from the Illumina website and merge it in R with the PLINK plugin output replacing the incorrect cM values in the .map file provided by the PLINK plugin for the correct ones in the .txt file.
Hi James, Have been struggling with this for a while now. Glad to see this thread. Please can you share the merged/updated file?
sure, leave your email address and ill send it through.