Former User of DNAx Community_33

Thank you for this. Do you have any experience with using WES for Step 2 of Regenie versus imputed data? Will that make a difference? It seems to me that using exome data would focus more on exomes...

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• 06 November 2023 16:27
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Hi, Phil! Thanks for all the work doing these tutorials and scripts. I'm trying to do a study of chronic imbalance, using genotype calls for Step 1 of Regenie, then WES for Step 2, did all the lift...

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• 05 November 2023 19:57
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Results of fewer SNPs total after using PJ Greer's scripts for Regenie using Plink genotype calls and final WES.

I used PJ Greer's scripts to perform GWAS, using my phenotype on UKB RAP, genotype array data, then the full final exome sequencing for step 2. I did (as far as I know) all the quality control step...

• Former User of DNAx Community_33
• 24 October 2023 00:00
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Thanks! We figured out the answer, but others might be interested.

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• 16 February 2023 16:22
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This is more of a question along the same lines. How do I fashion a manifest file to extract these VCF's. I have a list of eid's, but no way of matching them to the file-names. Thank you.

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• 15 February 2023 20:56
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Hi, Anastazie: Thank you for answering. I used the Eigensoft Tool in the Tools library, using files in my March 25, 2022 /Data folder. I have an entire slew of job failure reports, and it is case #...

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• 28 July 2022 02:28
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on array data. I'm looking to use the CONVERTF to convert plink files to Eigensoft files. I've tried creating .ped files, but somehow I get multiple errors. Thanks for answering.

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• 26 July 2022 15:10
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