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bjarke....@gmail.com
Nov 4, 2019, 9:09:11 AM11/4/19
to FUMA GWAS users
Hi Kyoko,
Thanks for a great tool.
It appears that eQTL results for GTEx/v8 are not completely captured by FUMA for some loci.
Toy example:
rs12750733 is an eQTL for several tissues in GTEx/v8 when looking it up at the GTExPortal. However, it does not appear in my FUMA runs, neither in the eQTL results table nor in the regional plot with eQTL annotation. The corresponding GTEx/v7 results are there.
Sincerely,
Bjarke Feenstra
Kyoko Watanabe
Nov 4, 2019, 9:13:15 AM11/4/19
to FUMA GWAS users
Hi Bjarke,
Thank you for your message.
Yes, I just realized today that there was some error in the script for liftover (since GTEx v8 was only provided in hg38 but FUMA is hg19).
I'm sorry about that!!
I'm fixing this right now, and will update online asap.
Should be able to do that by tomorrow latest and I will update you once it's done.
Best,
Kyoko
bjarke....@gmail.com
Nov 4, 2019, 9:17:43 AM11/4/19
to FUMA GWAS users
That sounds great - thank you very much!
Best,
Bjarke
Kyoko Watanabe
Nov 4, 2019, 3:02:52 PM11/4/19
to FUMA GWAS users
Hi Bjarke,
The issue has been fixed in FUMA v1.3.5e.
Let me know if you have any further questions.
Best,
Kyoko
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