I am attempting to execute Hail commands for performing VEP annotations and exporting the output. Despite trying multiple iterations, I am uncertain about the destination of the output. I have been following the tutorial code as recommended. Although I've created a table, I'm unsure how to export it as an output for analysis in R. Could you assist me with this?
Thank you for your help, and I eagerly await your response.
Regards
Akhil
I am running everything based on the tutorial mentioned above but it is not clear how to export the file from dnax database to the VM I am using to operate.
Thank you so much for the help. I have used that script to perform all the analysis and wrote the file to dnax as mentioned. Now my issue is I dont know how to pull data from Dnax to my workspace in jupyter notebook. Do we have a code snippet for that? Is it the same as extracting phenotypes from the database?
In case you already stored the annotated Hail object in dnax, just load/read the dnax context back to Hail (you can use the same notebook or begin your work in a new notebook, as the data is stored in permanent storage). I would try to use the hl.read_table() func as it is shown here: https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/gwas_ann_haildb.ipynb
Following up on this. I can't seem to get the code to copy files from HDFS to the VM environment and then to the project work from this tutorial https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/export_bgen.ipynb. Could it be that that tutorial is dated and/or things have changed in DNAnexus? Any suggestions?
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I can't say things specific to annotation step, but I tried out these notebook and they are handy with handling input/output from Hail.
https://github.com/dnanexus/OpenBio/tree/master/hail_tutorial
I am running everything based on the tutorial mentioned above but it is not clear how to export the file from dnax database to the VM I am using to operate.
@Ondrej Klempir?
Are we talking about this notebook? https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/MatrixTable_variant_annotation_with_VEP.ipynb
If so, dnax database behaves as a normal Hail Spark object/dataframe, you should be able to export the dataframe content to csv or txt.
Thank you so much for the help. I have used that script to perform all the analysis and wrote the file to dnax as mentioned. Now my issue is I dont know how to pull data from Dnax to my workspace in jupyter notebook. Do we have a code snippet for that? Is it the same as extracting phenotypes from the database?
I believe you have two main options now:
how to write export files to project out of dnax database?
try the method shown here: https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/export_bgen.ipynb
would recommended reading the parts 4) Copy files from HDFS and 5) Upload files to project
Following up on this. I can't seem to get the code to copy files from HDFS to the VM environment and then to the project work from this tutorial https://github.com/dnanexus/OpenBio/blob/master/hail_tutorial/export_bgen.ipynb. Could it be that that tutorial is dated and/or things have changed in DNAnexus? Any suggestions?
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