How to use Ensembl Variant Effect Predictor(VEP) on UKB data for GWAS? Former User of DNAx Community_24 23 March 2022 00:00 1 comment I am currently trying to run a GWAS pipeline on UKB data. We have converted data to hail matrix table. However, I am facing challenges due to VEP docker image not being accessible in worker nodes. Comments 1 comment Sort by Date Votes Ondrej Klempir DNAnexus Team 29 March 2022 10:51 Hi, In Spark based JupyterLab, specifying HAIL via "-ifeature" and "instance-count" might help to load the VEP docker image. dx run app-dxjupyterlab_spark_cluster -ifeature="HAIL-0.2.78-VEP-1.0.3" --instance-count=3 --instance-type mem1_ssd1_v2_x16 0 Please sign in to leave a comment.
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Hi,
In Spark based JupyterLab, specifying HAIL via "-ifeature" and "instance-count" might help to load the VEP docker image.
dx run app-dxjupyterlab_spark_cluster -ifeature="HAIL-0.2.78-VEP-1.0.3" --instance-count=3 --instance-type mem1_ssd1_v2_x16
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