I want to liftover the genotype array calls from hg37 to hg38. I reviewed the DNAnexus liftover GitHub but I am still unsure how to perform the liftover.
So far I have created a folder in my project, where I uploaded the following files: 1000genomes.grch38.fasta-index.tar.gz, b37ToHg38.over.chain, dxCompiler-2.10.2.jar and liftover_plink_beds.wdl. I have also installed the dx command line toolkit and I am able to log in and select the project of interest. I also loaded java on my terminal (java 15.0.2).
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When I run this command: java -jar dxCompiler-2.10.2.jar compile liftover_plink_beds.wdl -project pro
ject-{ID}.
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I get the following error: Error: Unable to access jarfile dxCompiler-2.10.2.jar
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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 data, it is a total of 6 scrips split between GT prep and GT liftover. Please give it a try.
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Did you install dxCompiler on your computer? It has to be on your computer, not in the UKB RAP project folder.
@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 data, it is a total of 6 scrips split between GT prep and GT liftover. Please give it a try.
https://github.com/pjgreer/ukb-rap-tools
Thanks @Phil Greer?! Will try this out
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