running non human WGS analysis
Hi! i want to run WGS analysis on thousands of samples of candida auris genomes in order to find variants associated with violence and drug resistance. the analysis requires preprocessing of the fastq files (fastqc, multiqc and trimming) and variant calling. i am fairly new to the cloud and not fully familiar with its applications, i would like to explore the option of using preconfigured workflows. however, the gatk variant calling workflow "GATK best practices for germline SNPs and Indels" is designed for human genomes and requires inputs the dont exist in candida auris genomes. i also couldnt find a fitting workflow in dockstore. i would like to know whether it is possible to use the preconfigured workflow designed for human and modify it in the cloud, and if so how can it be done. if this option is problematic, can i create a new workflow from scrath fitting my data? overall i would like to hear what is the best approach to run my analysis on the cloud.
thank you!
Comments
1 comment
Hi Naama Yefet! Thanks for reaching out about your analysis needs on Terra. It is definitely possible to modify GATK best practice workflows for non-human samples to run in the cloud on Terra. I believe the Darwin's Ark group runs their analyses in Terra, for example. However, that is out of scope for this forum, which is focused on Terra-focused questions about the platform itself.
If you need help modifying the WDL itself (as well as inputs such as reference files) for your use case, you may find help by posting your question on the GATK forum. See this post about a bacteria analysis, for example.
Some resources for editing WDLs that may be helpful include the following.
Hope this gives you a good start, Allie Cliffe
Please sign in to leave a comment.