Former User of DNAx Community_28

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 ...

• 28 November 2022 00:00
• 3 followers
• 7 comments
• 0 votes

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...

• 05 August 2022 00:00
• 3 followers
• 3 comments
• 0 votes

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...

• 04 August 2022 00:00
• 2 followers
• 2 comments
• 0 votes

What's the best way to find allele frequency for a variant in the WES data?

• 01 August 2022 00:00
• 2 followers
• 7 comments
• 1 vote