Former User of DNAx Community_28
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Recent activity by Former User of DNAx Community_28
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The next script 15a runs a gwas on each chromosome. ?16a combines all the results together.
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You need to generate a phenotype file, upload it to your project, and replace the name in the script with? the name you gave your phenotype file. The same will be true for the covariate file.?
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I just updated the README files for clearer explanation. see both the base readme as well as the gwas readme.https://github.com/pjgreer/ukb-rap-toolsandhttps://github.com/pjgreer/ukb-rap-tools/tree...
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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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