Former User of DNAx Community_4
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Recent activity by Former User of DNAx Community_4
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How to run VEP docker image using swiss-army-knife?
Hi, So I've been trying for the past few months to annotate my vcfs with VEP. I've managed to do this using docker rather than hail. However, I want to loop my docker annotation command through mul...
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- 4 comments
- 0 votes
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Best strategy for annotating and filtering VCF files using VEP on UKB RAP?
I've been struggling with a few issues regarding annotating VCF files on UKB RAP using HAIL. I am trying to annotate pVCF files that I subsetted using BCFtools and QC'd using VCFtools . The files a...
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- 0 votes
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How to export a matrix table as a VCF file after annotation on UKB RAP using HAIL?
I want to export my annotated matrix table as a vcf file as I want to filter my variants on my own server and not on DNAnexus. In order to export as a vcf I had to manually select which annotations...
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Can you annotate with CADD, gnomad, clinvar and dbNSFP options when using hail on Spark jupyterlab notebooks?
I'm just wondering how to specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster? From the hail website, the following command can be used on your ...
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- 2 comments
- 0 votes
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Where is dxjupyterlab-vep on spark cluster with HAIL-VEP? Cache is not found either.
So I'm trying to annotate my quality controlled pVCF files on UKB-RAP. I'm using a mem3_ssd2_v2_x16 spark cluster instance with HAIL-0.2.78-VEP-1.03. The main error I'm getting is that the path to...
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- 4 comments
- 0 votes
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How do I load .p.vcf.gz files into the python environment on the spark cluster? Do I need to use dxdata?
I want to annotate the files but can't find the documentation on actually loading the file into the environment. This documentation gives a rough outline of how to annotate (not precise) but it doe...
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- 3 comments
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