Computational biology and genomics
If you are planning on running some of the GATK workflows locally you will require various reference files, known as the Resource Bundle. Initially I had downloaded the files using FTP but I later realised various files were missing from the FTP server, such as BWA index and scatter files. Only later did I realise…
An approach I like to use when learning a new tool is to get started by trying to run an example and then gradually work out the details. In this post, I’m trying to learn the basics of the Workflow Description Language (WDL) so that I can adapt GATK workflows for my own use. WDL,…
The Broad Institute have shared their GATK workflows on GitHub, however they are configured to be used with Google Cloud. I was not able to find a lot of information on executing the workflows locally and I only found this tutorial. I ran into problems while trying to follow the tutorial but eventually got it…