I found dosage files from imputation. Are the corresponding confidence/quality scores available as well?
Thanks,
Ellen
Created by etsai Hi Lei @leiyu ,
I am using the imputed dosage files from Affymetrix and Illumina genotype data. Is it possible to get the info file for R^2 value to select SNPs that pass a particular threshold?
We are seeing a lot of NAs in the imputed data. Do you know why?
Thank you,
Sithara Hi Jian,
The clinical data uploaded to Synapse currently are restricted to those autopsied cases. To obtain same data for individuals with GWAS (both alive and deceased), please request through RADC data/resource sharing hub at http://www.radc.rush.edu or email our data coordinator Greg Klein at Gregory_Klein@rush.edu.
Best
Lei Hi,
I would like to get the info score based on the dosage file which need an extra phenotype file. I found the clinical file (syn3191087), however some of the individuals from *.fam file (syn5879839) were missing in the clinical file. Where can I find the complete information?
Thanks for your time
Jian
Hi Lei,
Thanks for your help. I was able to estimate the INFO scores now.
In addition to selecting a phenotype, I had add after the **--dosage chr_dose.gz** the parameters **noheader format=1** .
Looking forward to the latest imputation files, but this will do nicely.
Best Regards,
Ellen Ellen, the info scores are available in the plink GWAS output (using dosage imputed by Beagle). Just throw in a separate phenotype file (say age). Happy to share the script or upload files that contain info scores. Realistically probably by the end of the year or maybe early next year.
-Ben Thank you @ben.logsdon! That is great news. Do you have recommendations on how to watch for this update or a timeline for me (a few days, weeks, months, etc)?
Thanks again,
Ellen
Hi Ellen,
Yes, we will be uploading the new imputation data soon and will be able to provide the additional QC metrics at that point.
Ben Thank you for the comments. It would be nice to get new imputation data if it's available, especially for the reason below.
Hi @leiyu I don't believe beagle dosage files can be loaded into plink, nor could the INFO scores be obtained from these files. This dosage file format only contains SnpID and a corresponding dosage for each sample in each column. I look a quick look at the BEAGLE 3.3.2 documentation, the software version used by syn3157329. Could the Allelic R^2 file be provided?
Thanks,
Ellen Hi Ben and Ellen, INFO scores for dosage data can be obtained using plink (http://zzz.bwh.harvard.edu/plink/dosage.shtml) Hi Ellen,
I'm not sure, @leiyu are these available? Also @sieberts do we have these for the reimputation of the data?
Thanks,
Ben
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