Former User of DNAx Community_28

Thanks @Chai Fungtammasan? ! I was able to get the table with participant ID table

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• 02 December 2022 22:19
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Table exporter failed when I tried calling "eid"

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• 28 November 2022 19:09
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I want to run a PheWAS analysis using PHESANT and currently trying to generate the phenotype file. I am using table exporter to extract the phenotype data for my variables of interest.

My input is the entire phenotype dataset, and a field names text file (with 1000s field names, such as p30630_i0, etc).   The output file I am getting has columns corresponding to each phenotype ...

• Former User of DNAx Community_28
• 28 November 2022 00:00
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Thanks @Phil Greer?! Will try this out

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• 24 August 2022 18:41
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I want to liftover the genotype array calls from hg37 to hg38. I reviewed the DNAnexus liftover GitHub but I am still unsure how to perform the liftover.

So far I have created a folder in my project, where I uploaded the following files: 1000genomes.grch38.fasta-index.tar.gz, b37ToHg38.over.chain, dxCompiler-2.10.2.jar and liftover_plink_beds.wdl. I...

• Former User of DNAx Community_28
• 05 August 2022 00:00
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Hi Ben, I want to perform a liftover of the genotype calls and from my understanding need to use WDL workflows. I wanted to get your advice on how to set it up. I found this GitHub page (https://gi...

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• 04 August 2022 20:22
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Thank you!

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• 04 August 2022 18:27
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I am performing QC as per the AD-by-proxy-GWAS guide. For this, I need to load the WES files into my JupyterNotebook but I keep getting an error.

I selected one of the files under the WES plink format folder, and clicked copy path. Example below: path_to_family_file = '/project-{string of letters which is the project ID}:/Bulk/Exome seque...

• Former User of DNAx Community_28
• 04 August 2022 00:00
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Thanks! That fixed the error ?

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• 02 August 2022 14:55
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