Ondrej Klempir DNAnexus Team
Comments
Recent activity by Ondrej Klempir
-
Another option is to use Hail. Sharing here an example notebook which performs GWAS (tips on Create pheno Table is part of it): https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/gwas.ipynb
- View comment
- 0 votes
-
How to filter Genomic Data with Hail: Chromosomes and Positionshttps://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/filter_chrpos.ipynb
- View comment
- 0 votes
-
A) For applications, when you would like to combine geno and pheno data, there is a guide on how is the filename convention for Bulk data looks like https://dnanexus.gitbook.io/uk-biobank-rap/getti...
- View comment
- 0 votes
-
I do not have any example of such command ready to use. I think you can develop some testing commands based on this doc page: https://www.cog-genomics.org/plink/1.9/filter
- View comment
- 0 votes
-
pVCF is a population VCF which contains variant information from multiple samples, it has form of a big VCF table. Depending on which UKB WGS dataset you have access to, you may find pVCFs in the d...
- View comment
- 0 votes
-
OK. I do not think there is one only correct method how to analyze pVCF or how to answer your question about rs56041637. But pVCFs might be a good resource how to start with this. I would first con...
- View comment
- 0 votes
-
The following steps worked on my side: A) First go to the notebook and install plotly dependencies, including dependencies for JupyterLab: %%bashpip install plotly==5.14.1pip install "jupyterlab>=3...
- View comment
- 0 votes
-
Which WGS dataset are you referring to? In case a pVCF is available for filtering a specific variant, I would apply some filtering e.g. using Hail. In case there is no pVCF, there might be a reason...
- View comment
- 0 votes
-
Do you use JupyterLab or RStudio?
- View comment
- 0 votes
-
I am sharing here my findings on how I was able to access SQL query for CB cohort. Prerequisites: I created my cohort by applying filter in Cohort Browser (filter on specific age range), saved it a...
- View comment
- 0 votes