Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Somatic mutation calling - PON vs VCF
I have a dog tumor sample without matched normal. I know that it is recommended to have matched normal but for this specific data, it is not possible to get a matched normal sample.
I see that in GATK4-Mutect2 workflow, arguments (-normal, -pon, --germline-resource) are not mandatory. Therefore, technically I should be able to run Mutect2 with tumor sample and any of the available resources corresponding to normal (i.e. -normal, -pon, --germline-resource). Is this correct?
I am planning to use the BROAD's 435 dogs SNP/INDELS VCF to filter germline mutations in addition to ENSEMBL variants. Would this be a feasible approach in absence of matched normal?
Although I have the VCF file for 435 dogs, would it be helpful creating additional PON with the same 435 dogs data. I am not sure if PON with same data may provide some additional benefit in addition to VCF. OR generating PON with GATK4 may have improved calls as compared to older versions.
My tumor sample is from the Golden Retriever dog. If I am creating PON, do you recommend to use normal only from the same breed OR it is fine to mix breeds (i.e. PON with 435 dogs data).