Ondrej Klempir DNAnexus Team
Comments
Recent activity by Ondrej Klempir
-
What is the name of your database in DNAnexus project? Is it Chromosome19_b0_v1?What is in the mt_name variable?What is in the db_uri variable?
- View comment
- 0 votes
-
See the recent thread showing the Hail functionality and how to analyze genomics data using Hail:https://community.dnanexus.com/s/question/0D5t0000043xrVhCAI/hail-tutorial-and-example-notebooks-for...
- View comment
- 0 votes
-
This sounds to me as a possibly good candidate for download agent tool.https://documentation.dnanexus.com/downloads#download-agent Details are here:https://github.com/dnanexus/dxda/blob/master/READ...
- View comment
- 0 votes
-
I know that @Mike Tran? recently performed some nice SAIGE experiments, so maybe he will know. Since this seems to me more as a question for SAIGE team, you might also ask here: https://github.com/...
- View comment
- 0 votes
-
Hi Delnaz, Can this be related to this documention page? https://dnanexus.gitbook.io/uk-biobank-rap/frequently-asked-questions#data-has-been-dispensed-to-my-project-but-not-all-the-data-i-am-expect...
- View comment
- 0 votes
-
I think this would depend on your use case. You should be able to work with individual VCFs as well as with pVCF files. One of the suggestions would be to use Swiss Army Knife with vcftools and do ...
- View comment
- 0 votes
-
There is a possibility to handle intermediate workflow outputs using a custom reorg applet:https://github.com/dnanexus/dxCompiler/blob/develop/doc/ExpertOptions.md#handling-intermediate-workflow-ou...
- View comment
- 0 votes
-
One documention on workflow you proposed sits here: https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/gwas.ipynb It is a python Hail GWAS tutorial, demonstrating how to combine pheno an...
- View comment
- 0 votes
-
You may of course include more steps, e.g. filtering for specific pos: https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/filter_chrpos.ipynb
- View comment
- 0 votes
-
Hello @Esphie Fojas?, sure thing! I am also personally interested in this topic and I am wondering whether a step by step tutorial on this (of course a simplified version of the whole thing) would ...
- View comment
- 0 votes