Ondrej Klempir DNAnexus Team
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Recent activity by Ondrej Klempir
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Are you able to filter it and save just a subset of rows of your Spark df? Is it possible to first convert your Spark df to Pandas df and save? How big are the Hail GWAS results? Is it just one ch...
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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"...
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Two ideas:a. SAIGE might not be accustomed to be used for sex chromosomes.b. It seems there is an issue with the formatting of the group file: https://github.com/weizhouUMICH/SAIGE/issues/56 Alexan...
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Hi @Rachel Visontay?, I do not have much practical experience with running SAK in GUI batch mode, but I was able to locate the following setting for SAK: I assume that you will define all bgen inpu...
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Yeah, you will need to select an instance type with sufficient capacity of storage and memory. Here is a list of instance types:https://dnanexus-prod-asg-dnanexusprodassets4d7ed69b-i607e894f3ya.s3....
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I would write a submission script which would either 1) run the Swiss Army Knife separately for each chrom or 2) process bgens sequentially one by one. You should be able to provide a shell script ...
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I was able to reproduce this issue with the recent version of qctool. It worked well with an example small bgen, however, it failed when inputting a larger UKB bgen file. This seems to me as a bug ...
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If you want to provide more additional testing and experiment more with dxfuse on your local machine, this is what I would try: I would download some small publicly available vcf.gz and upload it t...
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Hi @Pierre LIndenbaum?, I would first try dxfuse-mnt. Samtools should be compatible with mnt sequential read. Please seehttps://community.dnanexus.com/s/question/0D5t0000045Gx4GCAS/extract-multiple...
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Thank you @Alexandra Lee?, @Chai Fungtammasan? and @Ben Busby? for contributing to this Tools and Tutorial post.
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