Former User of DNAx Community_4

Hi @Ondrej Klempir?,  Yes I found a solution by running a loop in VEP docker container. It is a slower approach but trying to run the docker image through swiss-army-knife was proving too difficult...

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• 26 July 2022 15:14
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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...

• Former User of DNAx Community_4
• 08 July 2022 00:00
• 3 followers
• 4 comments
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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...

• Former User of DNAx Community_4
• 10 June 2022 00:00
• 1 follower
• 1 comment
• 0 votes

Hi Ondrej,  Yes I was able to solve this by changing gs to aws and I kept the region as US.

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• 26 May 2022 15:10
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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...

• Former User of DNAx Community_4
• 26 May 2022 00:00
• 1 follower
• 1 comment
• 0 votes

I figured out the issue with help from Matej. So yes the custom .json file was not correctly formatted but also the .json file needs to be stored in the root directory and not in a subfolder. Than...

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• 06 May 2022 13:24
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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 ...

• Former User of DNAx Community_4
• 06 May 2022 00:00
• 2 followers
• 2 comments
• 0 votes

Hi Ondrej,  I'm using three nodes. I got this error message on the python 3 console: Error summary: HailException: VEP command 'docker run -i -v /cluster/vep:/root/.vep dnanexus/dxjupyterlab-vep ./...

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• 19 April 2022 10:36
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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...

• Former User of DNAx Community_4
• 14 April 2022 00:00
• 2 followers
• 4 comments
• 0 votes