I am hoping I can have a script to run SAIGE GWAS on Dx command line using bgen files. Best- Nihal

21 December 2022 00:00
3 comments

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 files: saige_step1_ukb_cal_chr1_22_v2_merged.rda saige_step1_ukb_cal_chr1_22_v2_merged.varianceRatio.txt

Comments

3 comments

Chai Fungtammasan DNAnexus Team
- 21 December 2022 05:39
Do you want to try out this tutorial which use PLINK? https://community.dnanexus.com/s/question/0D5t0000046y0ZHCAY/analyzing-uk-biobank-wes-data-using-saigegene
You can use swiss-army-knife to convert bgen to plink.

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Former User of DNAx Community_91
- 22 December 2022 12:18
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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Chai Fungtammasan DNAnexus Team
- 22 December 2022 21:10
I think the approach in the tutorial should work for all chromosomes.

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