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JonJala
snpID format
Hi, I am still having trouble running MTAG this is the error i am getting when I run my summary stats, ValueError: After merging with reference panel LD, 0 SNPs remain. which I am guessing is due to my SNP not being in the formart MTAG recognizes, my snpIDs are like this (chr12:28175:G:GT) does MTAG only accepts rsIDs? another question is where can I download the summary stats used in the tutorial found on the wiki? Thank you
The SNP IDs of the reference panel and the summary statistics have to match. Otherwise MTAG won't know which SNP is which. So you'll have to find some reference panel that links the SNP IDs between the two and replace that column.
For the tutorial data, thanks for bringing this to our attention. It looks like the links were broken when the SSGAC moved their summary statistics to thessgac.com, but I'm not sure the test data for the tutorial was migrated. We'll try to get it up and running as soon as we can.
On Thu, Sep 14, 2023 at 7:22 AM AudeIkuzwe @.***> wrote:
Hi, I am still having trouble running MTAG this is the error i am getting when I run my summary stats, ValueError: After merging with reference panel LD, 0 SNPs remain. which I am guessing is due to my SNP not being in the formart MTAG recognizes, my snpIDs are like this (chr12:28175:G:GT) does MTAG only accepts rsIDs? another question is where can I download the summary stats used in the tutorial found on the wiki? Thank you
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Just updated the tutorial to point to thessgac.com. It does require registering for an account, but once that is done, then just download the Okbay et. al. 2016 summary stats for neuroticism and subjective well-being that the tutorial indicates.
Hi, you mentioned a 'reference panel'. Would you suggest converting chromosomal positions (chr:bpos) into rsids for this. For example by using the UCSC database? Or is it possible to use chromosomal positions instead of rsids in MTAG. Thanks!
