Former User of DNAx Community_28
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Recent activity by Former User of DNAx Community_28
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I mainly use linux/mac, so I am not familiar with windows environment variables. try:https://www.alphr.com/clear-environment-variables-windows/or https://www.digitalcitizen.life/remove-edit-clear-...
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Are you logged in via the dx toolkit and have a default project selected? https://documentation.dnanexus.com/getting-started/cli-quickstart
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This comment was left over from the scripts I was using to create these sets. The imputed plink gwas is standalone and does not require any prior steps other than: install dx toolkit. login with d...
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Alternatively, you can extract the snp from the bgen file using bgenix via swiss-army-knife. Then read the single snp bgen with plink and export out as a raw file. The raw file will have the fid ii...
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if 15a ran and you should have the *.glm.logistic.hybrid files in your data directory, you need to make sure that the -iin file is points to the correctly names outfile from step15a. It will like...
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Chai, No, that is really the bare minimum information. The original HRC imputation paper (https://biobank.ndph.ox.ac.uk/showcase/refer.cgi?id=530) and the GEL pdf (https://biobank.ndph.ox.ac.uk/sh...
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I updated my GWAS repo for TOPmed imputed data using plink. I will work on adding the regenie version sometime in the near future. https://github.com/pjgreer/ukb-rap-tools/tree/main/GWAS_pipeline/g...
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You also need to make a couple of directories in your project, $data_file_dir for the directory you will put your data, and a $txt_file_dir where all the phenotype files will be stored. If those d...
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{@005t000000149vjAAA}? is pointing to some more advanced tools like docker, batch processing, WDL workflows etc. Those advanced tools are great and you should definitely look into those once you a...
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@Niyati Jain? , If you haven't worked this out yet, I posted a github repo of shell scripts that will allow you to run liftover independent of the WDL script. For liftover on the genotype array dat...
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