Former User of DNAx Community_91

Thank you Phil!

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• 02 March 2023 19:56
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Thank you Phil so much!I saw this very helpful thread.  I am thinking that I need the QC steps to remove individuals with missingness, relatedness, sex-genetic mismatch. And also remove these vari...

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• 02 March 2023 19:45
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Hi- I ran the GWAS analysis using SAIGE and I had a very nosiy QQ plot and Manhattan plot. I just realized that I have not run QC steps on the imputed data. Is there a good resource on the QC steps before SAIGE analyses? Best- Nihal

• Former User of DNAx Community_91
• 28 February 2023 00:00
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Thank you for your response. I am trying to run SAIGE,. I have it run for one chromosome but I would like to run for the 22 chromosomes.  Best-Nihal

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• 22 December 2022 12:18
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I am hoping I can have a script to run SAIGE GWAS on Dx command line using bgen files. Best- Nihal

The sample file: ukb22828_c1_b0_v3_sample.txt (there is a file for each chr) The bgen file: ukb22828_c22_b0_v3.bgen (there is a file for each chr) The Bgi file: ukb22828_c22_b0_v3.bgen.bgi   Other...

• Former User of DNAx Community_91
• 21 December 2022 00:00
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